Great project. However, I'm not comfortable with the need to keep data in memory. It seems like you could get past that by augmenting your checkpointing code, making it easier and more effective to save the current state of work. It seems like you'd want to run that checkpointing code just before the computer shuts down (if you're running then) and just before you relinquish the processor to another BOINC project.

Maybe there's information that'll make me more comfortable with leaving data in memory. Do you tie up only a "small" amount of memory? Does Windows put that data in the swap file on disk if you don't happen to be running?