This is most likely not a bug in MegaGlest. Please consider filing a bug report against your distribution's driver / mesa packages, as well as upgrading to a newer version of your distribution (or newer Kernel / X / MESA / driver stack), if possible.
You did not disclose which Linux distribution (and version) you are using. Since you're saying you're using the MegaGlest package from Debian Wheezy, I assume this is the distribution and version you are using, but with a more current kernel image. I suggest you also try this with Wheezy's default Kernel image which seems to be based on Linux v3.2.0.
You can also try some workarounds on MegaGlest (some of which are discussed in the
FAQ, too):
- megaglest --disable-vbo
- export SDL_MOUSE_RELATIVE=0; megaglest
- Set No2DMouseRendering=1 in glestuser.ini
Note that with packaged installation, the ini file location may not be ~/.megaglest/glestuser.ini but ~/.config/megaglest/glestuser.ini (I just don't remember where the Debian packages put it).
If none of this works, please try MegaGlest 3.7.1. You can use the installer we provide on
http://megaglest.org (hosted on sourceforge), which will place all files in ~/megaglest by default. Or you can download separate data + binary archives (references to which may be found on the bottom of the Downloads page). If you go with the latter option, extract the data archive first, then change into the extracted directory and extract the binary archive there (or use tar -C ...).
Then try both the standard configuration as well as these workarounds on 3.7.1.
If this does not help either, then you can try a
current snapshot (3.8.0-dev), repeating all tests. It's currently sufficient to extract the binary archive to the 3.7.1 installation directory, you do not need to download and replace the game data for testing.
Whenever you test, be sure to deactivate the 3D related options in the options menu to rule out side effects.
Possibly related reports:
[not a bug] v3.6.0, radeon: Mouse clicks are registered at bottom of screenProblems with Intel driver in linux [solved]