Windows 2000 crashes while copying video files

I have noticed that sometimes when moving/coping multiple video files of various formats (mpg,avi, etc) that windows will restart itself. When it tries to boot, I get the message NTLDR is missing. When I boot with a boot disk and look at whats on the boot drive, all that shows up for file and folder names are a bunch of random symbols, letters and numbers. I have had this happen multiple times, and my usual responce is to format the drive and reinstall (I have a partition for windows alone, just for reasons like this). It seems that when the crash occurs, my E partition is removed(luckily I always install my games there). I use 2 harddrives, 1 160g and 1 80g, the 160 being the master and both having 4 partitions. Therefore the E partition is the second partition on the first drive. I have had various virus infections in the past, but they should have all been cleaned up and any files not able to be cleaned removed. I was wondering if this is a os error, or perhaps a video file is still infected or corrupted somehow. any help would be greatly appreciated on how to fix and prevent this problem. My system specs are as follows:

2600 AMD Athlon XP Processor
1g ram in the form of 2 paired 512 duel channel sticks
160g harddrive (boot and master drive)
80g harddrive (slave)
Windows 2000 (at the moment)