I have two Ubuntu Linux computers with Steam installed. For some games, cloud sync works fine for me at synchronizing my saves, but for some like SpaceChem and Faster Than Light it fails for me. When I started either on my second computer, it did not see my save.

I noticed that on my second computer, I have both "~/.local/share/zachtronics industries/spacechem" and "~/.local/share/Zachtronics Industries/SpaceChem" directories. Also "~/.local/share/fasterthanlight" and "~/.local/share/FasterThanLight" directories. The lower-case directories have my old steam-synced save files, but the games only use the latter title-case directories. On platforms like Windows and OS X, this would not be an issue because the filesystem is case insensitive and would treat both names as the same directory, but Linux is case sensitive and treats them as unrelated directories. Steam cloud sync appears to be converting the directory names to lower-case under the assumption that the system is case insensitive.

This issue doesn't happen for me for all of my games. The games that I have problems with cloud sync are only games that I've installed and played on OS X in the past. A game that I've only played on my two Linux computers (Infinifactory, by the same company as SpaceChem) does not show the issue, and works fine with cloud sync for me despite having a title-case directory ("~/.local/share/Infinifactory"). I believe the issue only happens if you've used cloud sync for that game on a non-Linux computer before.