Happens to me all the time.

I run a very processor intensive program while I'm asleep or at work and my clock falls back anywhere from 10 minutes to 5 hours everytime.

I believe it has to do with the fact that the program I use, uses almost 100% of system resources which in turn takes resources away from the clock.

I never considered it to be a big deal as the clock stays right on time if I'm not using that particular program.

I just reset it and go on my way.

By the way, rereading your post, the program I use is also a ftp type program, more like a P2P program, but mostly same function, ie: downloading/uploading. My system is a Pent II, 400mhz, 512 ram. I also didn't have this problem when I got the computer 4 years ago, but I also was not downloading/uploading the quanity of material I am now.