The recurrence of that bug on your system is outstanding. I think it might not be related to your C2 install and rather be an influence of your system config or a program running in background..!
To be sure about this, could you simply give the Vanilla C2 pack a quick try? You can download it at this address: http://rr2000.toshiba-3.com/R4/PC/vanillac2_r1b.zip It just requires a glide wrapper to run, if you already have nGlide installed on your system you should be good to go. If the same symptoms appear, then I'd say the bug is triggered by another process running in the background or something like that.