I wonder if this is related to microcode? In Synaptic (Debian) there is a microcode update package. Search for it. If it's installed, try uninstalling it and if it's not installed, try installing it.
Running Linux shouldn't affect the bios, but it could affect bios settings. I know from experience with a colleagues Lenova Thinkpad that many of it's 'features' are bios based software that only run under Windows. (e.g. the on-screen keyboard) You should not have to flash the bios more than once in the machine's life-time though so this is a real problem.
Also, try going through the bios settings (accessed at power-on) and write down these settings immediately after re-flashing the bios. compare these with the settings after the problem manifests. If you see any changes, chances are that's the culprit!