I saw you ran fluxbox. Can you post your fluxbox --info information?

In Unity it's working as it should.

fluxbox --info

Fluxbox version: 1.3.2
Compiled: Nov 14 2011 10:51:25
Compiler: GCC
Compiler version: 4.6.2

Defaults:
menu: /etc/X11/fluxbox/fluxbox.menu-user
style: /usr/share/fluxbox/styles//ubuntu-light
keys: /etc/X11/fluxbox/keys
init: /etc/X11/fluxbox/init
nls: /usr/share/fluxbox/nls

Compiled options (- => disabled):
BIDI
-DEBUG
EWMH
IMLIB2
NLS
REMEMBER
RENDER
SHAPE
SLIT
TOOLBAR
XFT
XINERAMA
XMB
XPM

Ok, maybe not the exact same issue as mine ( #1287 ) but very similar issue.

I'm very sure this is a Fluxbox issue and not so much CS:S related. The same thing happens in TF2 right?

Can I see your ~/.fluxbox/init ?
Does the game work correctly in fullscreen?

Fullscreen works, same as changing resolution in fullscreen.

~/.fluxbox/init:

session.screen0.menu.alpha: 193
session.screen0.slit.layer: Dock
session.screen0.slit.onhead: 0
session.screen0.slit.acceptKdeDockapps: true
session.screen0.slit.autoHide: false
session.screen0.slit.placement: RightBottom
session.screen0.slit.alpha: 255
session.screen0.slit.maxOver: false
session.screen0.tab.placement: TopLeft
session.screen0.tab.width: 64
session.screen0.titlebar.left: Stick
session.screen0.titlebar.right: Minimize Maximize Close
session.screen0.toolbar.autoHide: false
session.screen0.toolbar.layer: Dock
session.screen0.toolbar.tools: prevworkspace, workspacename, nextworkspace, clock, prevwindow, nextwindow, iconbar
session.screen0.toolbar.maxOver: false
session.screen0.toolbar.visible: false
session.screen0.toolbar.alpha: 255
session.screen0.toolbar.height: 0
session.screen0.toolbar.placement: BottomCenter
session.screen0.toolbar.onhead: 1
session.screen0.toolbar.widthPercent: 100
session.screen0.window.focus.alpha: 255
session.screen0.window.unfocus.alpha: 255
session.screen0.iconbar.usePixmap: true
session.screen0.iconbar.mode: {static groups} (workspace)
session.screen0.iconbar.alignment: Relative
session.screen0.iconbar.iconWidth: 128
session.screen0.iconbar.iconTextPadding: 10
session.screen0.clientMenu.usePixmap: true
session.screen0.tabs.usePixmap: true
session.screen0.tabs.maxOver: false
session.screen0.tabs.intitlebar: true
session.screen0.opaqueMove: true
session.screen0.windowMenu: ~/.fluxbox/windowmenu
session.screen0.maxDisableResize: false
session.screen0.clickRaises: true
session.screen0.focusNewWindows: true
session.screen0.allowRemoteActions: false
session.screen0.workspaceNames: Workspace 1,Workspace 2,Workspace 3,Workspace 4,
session.screen0.noFocusWhileTypingDelay: 0
session.screen0.menuDelay: 200
session.screen0.strftimeFormat: %d %b, %a %02k:%M:%S
session.screen0.defaultDeco: NORMAL
session.screen0.rowPlacementDirection: LeftToRight
session.screen0.fullMaximization: false
session.screen0.workspacewarping: true
session.screen0.showwindowposition: false
session.screen0.focusModel: ClickFocus
session.screen0.colPlacementDirection: TopToBottom
session.screen0.maxIgnoreIncrement: true
session.screen0.workspaces: 4
session.screen0.windowPlacement: RowMinOverlapPlacement
session.screen0.tabFocusModel: ClickToTabFocus
session.screen0.autoRaise: true
session.screen0.maxDisableMove: false
session.screen0.edgeSnapThreshold: 10
session.screen0.tooltipDelay: 500
session.autoRaiseDelay: 250
session.cacheLife: 5
session.appsFile: ~/.fluxbox/apps
session.ignoreBorder: false
session.menuFile: ~/.fluxbox/menu
session.keyFile: ~/.fluxbox/keys
session.doubleClickInterval: 250
session.tabsAttachArea: Window
session.cacheMax: 200
session.slitlistFile: ~/.fluxbox/slitlist
session.forcePseudoTransparency: false
session.styleOverlay: ~/.fluxbox/overlay
session.styleFile: /usr/share/fluxbox/styles//ubuntu-light
session.tabPadding: 0
session.colorsPerChannel: 4
session.configVersion: 13

Oh man, maybe I didn't run it in windowed after all. I was just to excited to get it working that I forgot it test this.

Well, I just tried doing some stuff that I thought might fix this, but no :(

I'm pretty sure this issue is WM related though.

TF behaves same as CS:S.
GoldSrc games (HL and CS1.6) - OK.
Trine 2 - OK.
Polynomial - OK? (it's behaving weirdly when in window mode)
FTL - OK
World of Goo - OK
Cogs - OK
Amnesia - OK

Shouldn't be this tagged also with CS:S and TF2?

I was actually just looking into this.
I trying starting X only with a terminal

contents of xinitrc:
exec urxvt

then run command
startx

in urxvt, in the X session run steam
steam

Now, steam launches, and I start CS:S. It will then create a 640x480 image in the center, with black borders and not scale the image. Though CS:S itself will run 1920x1080 (looking at terminal output from Steam) which is compressed inside this little box. None of the buttons are clickable though.

I have this exact same issue with TF2, as well. I use the launch options -windowed -w 1600 -h 900 and can verify that the game does load assuming that resolution and in windowed mode (according to the video settings in-game), but the window itself is still 640x480. The window hints are also being set correctly (xwininfo):

WM_HINTS(WM_HINTS):
    Client accepts input or input focus: True
WM_NORMAL_HINTS(WM_SIZE_HINTS):
    user specified location: 960, 480
    program specified minimum size: 1600 by 900
    program specified maximum size: 1600 by 900

However the game loads with the incorrect geometry (xprop) geometry 640x481+1371+409. I can resize the window appropriately, which is a pain to get just right, but the resolution is correct even though the window size isn't.

I use i3, a tiling window manager, but set all Steam WM_CLASS matches to float automatically. And I'm sure my WM is respecting size hints as other applications like MPlayer hit floating mode with the correct size.

Processor Information:
Vendor: GenuineIntel
Speed: 3201 Mhz
12 logical processors
6 physical processors
HyperThreading: Supported
FCMOV: Supported
SSE2: Supported
SSE3: Supported
SSSE3: Supported
SSE4a: Unsupported
SSE41: Supported
SSE42: Supported

Network Information:
Network Speed:

Operating System Version:
Linux (64 bit)
Kernel Name: Linux
Kernel Version: 3.7.5-1-ARCH
X Server Vendor: The X.Org Foundation
X Server Release: 11302000
X Window Manager: LG3D (Actually i3)
Steam Runtime Version:

Video Card:
Driver: NVIDIA Corporation GeForce GTX 670/PCIe/SSE2

Driver Version:  4.3.0 NVIDIA 313.18
Desktop Color Depth: 24 bits per pixel
Monitor Refresh Rate: 59 Hz
VendorID:  0x10de
DeviceID:  0x1189
Number of Monitors:  2
Number of Logical Video Cards:  1
Primary Display Resolution:  2560 x 1440
Desktop Resolution: 5120 x 1440
Primary Display Size: 23.50" x 13.23"  (26.97" diag)
                                        59.7cm x 33.6cm  (68.5cm diag)
Primary Bus: PCI Express 16x
Primary VRAM: 4096 MB
Supported MSAA Modes:  2x 4x 8x 16x 

Sound card:
Audio device: Realtek ALC898

Memory:
RAM: 32158 Mb

Miscellaneous:
UI Language: English
LANG: en_US.utf8
Microphone: Not set
Total Hard Disk Space Available: 5394190 Mb
Largest Free Hard Disk Block: 3137941 Mb

WORKAROUND which worked for me (use on your own responsibility):

1. install wmctrl (sudo apt-get install wmctrl)
2. run game
3. wmctrl -r Counter-Strike -e 0,0,0,X,Y
   where X is your width and Y is your heigh resolution

example:
wmctrl -r Counter-Strike -e 0,0,0,1680,1050

Sadly i3 users, like myself, cannot employ wmctrl. But in the spirit of your workaround Roman, I'm going with this in my config:

for_window [title="Team Fortress 2 - OpenGL"] floating enable; resize grow right 960 px; resize grow down 420 px

That should help anyone else using i3. I'm just growing the window from 640x480 to the correct size. It works well, but one day when this gets fixed I'm sure I'll be shocked by the 2560x1320 window it renders.

No one is assigned, tags don't include TF2 or CS:S, no one is taking care. I'm thinking about reposting to Source-1-games hub, maybe there, maybe...

Please do @roman-bronis, this managed to get forgotten by the automated script because tags werent on it :(
It does appear to be an odd behaviour though; have you checked fluxbox bug tracker for similar problems?

It's affecting i3 also, so I don't think it's Fluxbox related. I'm going to repost it there.

EDIT: reposted here - https://github.com/ValveSoftware/Source-1-Games/issues/162

Handling this under the Source-1-Games issue - ValveSoftware/Source-1-Games#162