A similar phenomenon was occurring to Batman/JokerPCoc over on Number Crunching at one stage even without running ANY games. Eventually, In that case, we traced it to the XP default "Optimize Hard Disks When Idle" Background operation, which can be disabled using the "TweakUI PowerToy for XP" from Microsoft If you defragment externally every so often. It seems Boinc fairly constantly modifies files , so any active antivirus not set to exclude that folder, and background HD optimisation like the one mentioned would probably indeed kick in every approximately checkpoint interval.
Jason