I recently ran into a problem using Steam for Linux while playing Half-Life. It stopped syncing to the Steam Cloud after one of the Steam updates came through. So, I ended up having to continue playing on Windows.
After a bit of rummaging around on the web, I discovered there was a fix several months ago for this problem. Unfortunately, the fix was not being applied to my Steam client (it was related to the case of the save-game directory being incorrect, not a problem on Windows, since the file system is case insensitive. Linux file systems are usually case-sensitive, ie, "save" and "SAVE" are two different directories.)
Here is a quick hack to work around the problem:
Quit your Steam client.
Fire up a command line, and type:
ln -s SAVE save
Then restart your Steam Client.
I've checked this and it now syncs properly between Windows and Linux again.