this definitely sounds like there's been a problem writing to or reading from the hard disk.
When a FAT has become corrupted in the past, i've had trouble playing mp3s. They've become corrupt, and played ok up to a point, then there's been half a second from another song, or another song that's been deleted, like you describe.
Obviously, when a file gets deleted, it doesn't actually get overwritten, it just gets deleted from the FAT. If something hasn't properly been deleted from the FAT, but the sectors it uses have been overwritten, or the FAT is pointing to the wrong place, like you're describing, it can really balls things up.
Obviously, i'm talking about windows stuff here, but i'm assuming that macs use a file allocation table of sorts, and that it's becoming corrupted.
If i was getting stuff like this happening, i'd be thoroughly stress testing the memory, cpu and hard disk. Leave it testing for a week if need be. There's something very wrong there. My guess is, it's corrupted FATs.
AMD Athlon 1700 (@2200mhz from 1466 sod the noise!) - 768mb pc3200 - 200GB Maxtor - Pioneer 106 - GF4 Ti4200 - twinhan/visionplus pci dvb-t - random pci analogue tv tuner - A7v600-x (to replace the a7n8x-d that died...) - random 17\" CRT
Sony STR-DE425 & Eltax c205s;
xBox w/20GB HDD- executer 2.3b;
xBox - standard;
Konica/Minolta dimage z10 w/2x512mb SD;
A silly amount of Cat-5 and usb cables