Would you run steam in a terminal and provide the whole log of loading steam+SpaceChem so we can find out if its a Steam issue or not.

I bought SpaceChem with an humble bundle. I think it was the Humble Frozen Synapse Bundle.
The package from the humble bundle worked fine.
Then I redeemed it on Steam. I played it with Steam on a macbook with OSX10.6.8 before.
I don't have the DLC.

STEAM_RUNTIME is disabled automatically on Linux
Installing breakpad exception handler for appid(steam)/version(1359600063_client)
Installing breakpad exception handler for appid(steam)/version(1359600063_client)
unlinked 0 orphaned pipes
Installing breakpad exception handler for appid(steam)/version(1359600063_client)
[0202/020847:ERROR:object_proxy.cc(239)] Failed to call method: org.freedesktop.DBus.Error.ServiceUnknown: The name org.freedesktop.NetworkManager was not provided by any .service files
[0202/020847:WARNING:proxy_service.cc(646)] PAC support disabled because there is no system implementation
Installing breakpad exception handler for appid(steam)/version(1359600063_client)
Installing breakpad exception handler for appid(steam)/version(1359600063_client)
PulseAudio connect failed (used only for Mic Volume Control) with error: Access denied
Installing breakpad exception handler for appid(steam)/version(1359600063_client)
Installing breakpad exception handler for appid(steam)/version(1359600063_client)
Generating new string page texture 2: 48x256, total string texture memory is 49,15 KB
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Installing breakpad exception handler for appid(steam)/version(1359600063_client)
Installing breakpad exception handler for appid(steam)/version(1359600063_client)
Installing breakpad exception handler for appid(steam)/version(1359600063_client)
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roaming config store loaded successfully - 6082 bytes.
migrating temporary roaming config store
ExecCommandLine: "/home/user/Steam/ubuntu12_32/steam steam://run/92800"
ExecSteamURL: "steam://run/92800"
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Attempting to use a Windows only path root on non-Windows platform for game 92800
Attempting to use a Windows only path root on non-Windows platform for game 92800
System startup time: 12,94 seconds
STEAM_RUNTIME is disabled automatically on Linux
ExecCommandLine: "/home/user/.steam/root/ubuntu12_32/steam steam://open/driverhelperready"
ExecSteamURL: "steam://open/driverhelperready"
Attempting to use a Windows only path root on non-Windows platform for game 92800
Attempting to use a Windows only path root on non-Windows platform for game 92800
Failed to load installscript /home/user/Steam/SteamApps/common/SpaceChem/installscript.vdf
Attempting to use a Windows only path root on non-Windows platform for game 92800
Failed to resolve path before download

@nonno-cicala Odd, that makes it look like Steam is producing those errors but I do not see them here.
Wonder if its a problem related to spacechem & steamcloud, as you both have played before on other platforms.

OK, it seems to be a misconfiguration in SpaceChem’s cloud setup, it has no rootoverrides for linux users so its still looking for WinAppDataLocal.
Confirmed that with data in the cloud (thanks weltall), Steam produces these errors. With my empty steamcloud, its doesnt complain but also doesnt store anything ‐ which would explain the 0KB usage for the game.

yet some additions. the cloud error won't prevent the game from starting but just show a "your saves will go in the fire" warning (the classic unable to sync the cloud warning which happens when you relaunch a game too fast in normal situations) upon launching and prevent you from using the cloud content. At least for me.
Instead I had another problem: the game overrides completely the LD_LIBRARY_PATH in the launch script:

#!/bin/sh
LD_LIBRARY_PATH=~/.steam/bin:. MONO_CFG_DIR=etc MONO_PATH=monolib ./mono SpaceChem.exe

this will make the game fail if some library is missing in the system (32bit flavour)

#!/bin/sh
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/.steam/bin:. MONO_CFG_DIR=etc MONO_PATH=monolib ./mono SpaceChem.exe

this small change allows it to start on my system as I've all the required libraries in the previously set ld library path. namely in my case the library missing was libjpeg8 which is absent from both of the folders pointed by the ld_library_path override.

You should have a folder ~/.local/share/Zachtronics Industries/SpaceChem/crashes$ it contains the data about crashes from the game (they are simple compressed archives) in my case:
Exception:
System.DllNotFoundException: libSDL_image-1.2.so.0
at (wrapper managed-to-native) Tao.Sdl.SdlImage:IMG_Load (string)
at #=qdV4VjzCtWXVdyvykxllTXcaOJtEpqYyuviC2kQzmeFU=.#=q86ryNYpi1oYiBjWx4K9J1Q== (System.String #=qWgrL2JxwCEo79HA$n3N6vg==) [0x00000] in :0
at #=qnXizoHa4dN33EsdBlCLIeK0SZalNiwRqmxF1iN6o1FQ=.#=q3fNp4UpIVchWVbe0TywjQg== (System.String #=qIwVJspl5kO2$0pFePid06w==) [0x00000] in :0
at #=q1vI3mMcWvvIFqz$oyDDsIA==.#=q4lNuizBtSKCkY2vxyTu7AQ== () [0x00000] in :0
at #=qQdKRcUfE46$efAqMsrzhkw==.#=qtAieMJa3O4$ICce59T5vcg== () [0x00000] in :0

checking that library (with the proposed library path from the game) shown that libjpeg8 was missing
ldd libSDL_image-1.2.so.0
linux-gate.so.1 => (0xf77b7000)
libpng12.so.0 => /lib32/libpng12.so.0 (0xf7749000)
libjpeg.so.8 => not found
libtiff.so.4 => /usr/lib32/libtiff.so.4 (0xf76ee000)
libSDL-1.2.so.0 => /usr/lib32/libSDL-1.2.so.0 (0xf7665000)
libc.so.6 => /lib32/libc.so.6 (0xf7501000)
libz.so.1 => /usr/lib32/libz.so.1 (0xf74eb000)
libm.so.6 => /lib32/libm.so.6 (0xf74c5000)
libjpeg.so.62 => /usr/lib32/libjpeg.so.62 (0xf74a5000)
libasound.so.2 => /usr/lib32/libasound.so.2 (0xf73d9000)
librt.so.1 => /lib32/librt.so.1 (0xf73d0000)
libdl.so.2 => /lib32/libdl.so.2 (0xf73cb000)
libpthread.so.0 => /lib32/libpthread.so.0 (0xf73b2000)
/lib/ld-linux.so.2 (0xf77b8000)

so this is overriding even the steam-runtime (which i'm using forcefully as it works great)

Is this working now for the people with the windows-only path error?

Linking in a bug, #680 has users that reported this issue aswell.

LD_LIBRARY_PATH error is still there, i don't get the windows error anymore (maybe because the cloud is empty) but the cloud seems still not working (not uploading anything)

I'm still getting the message: "Attempting to use a Windows only path root on non-Windows platform for game 92800"
And I still receive the warning: "Steam was unable to sync your files for SpaceChem with the Steam Cloud"
I'm sorry that I was really hasty before, this was really my problem since the beginning but I don't want to risk to lose my progress so this prevents me from running the game.
Thank you for working on the issue.

well you won't as steam linux is unable to use the cloud at all, i'd be careful when they restore the functionlity in case (by fixing the configuration on steam servers). In order to not have your errors anymore you'd need to clean the steam cloud: http://forums.steampowered.com/forums/showthread.php?t=2470784 . this way steam won't trigger this bug.
also disabling it from the update tab should solve the issue (and save your saves) but to re enable it would be better doing a backup first.

SpaceChem’s ufs setting just got an update that should fix this, please test :)

The "Windows only path" problem is fixed, but the game didn't start unless I applied the LD_LIBRARY_PATH fix explained by weltall.
Now I have SpaceChem running with my data from the Steam Cloud. :)
Thank you all!

We're discussing the LD_LIBRARY_PATH overwriting with the developer, hope that'll get fixed soon.

Keith from Zachtronics here -- SpaceChem has been updated, and the LD_LIBRARY_PATH problem should now be fixed. Please give it a try and let me know if you still have problems.

LD_LIBRARY_PATH is fixed now but for me the cloud is still broken. i don't have XDG_DATA_HOME in my environment, in this case it silently doesn’t upload anything.
It seems also setting xdg data home by hand to $HOME/.local/share (which should be the default fallback) doesn't make it work. There are no errors but the data is never uploaded to the cloud

I don't have XDG_DATA_HOME in my environment but everything is working fine here. I did some progress in the game on Gentoo Linux and I found it on my macbook.

Closing this bug because LD_LIBRARY_PATH problem is fixed. Weltall, if you have a new bug to report please open a new one. Thanks.