A new patch has been released by Valve to fix this annoying problem
Valve has released Half-Life 2 and Portal for the Linux platform, but a few save corruption bugs have plagued the versions right from the start.Half-Life 2 and Portal for Linux have already received a large number of changes and improvements in the last few weeks, but a bug that corrupts the saves has proved itself quite resilient.
Reports about corrupted saves have been floating around for a few weeks now, and Valve was quit to take action. The bug still persisted and users have been unable to play the game properly.
This is to be expected, especially because both games are in the Beta stages and Valve can't guarantee that they will work properly.
A third patch designed to tackle this bug has been issued by Valve, so if you see that Portal and Half-Life 2 are updating, then you should know that it's this particular patch.