i used to have the same exact problem. it never cropped up until jaguar, and i had done a format and install. i think i figured out the problem tho. when i originally installed jaguar i formatted the drive, but did not reboot immediately afterwords. i wasnt prompted to, and i just forgot. the problem finally got so bad with the perpetual icon bounce that i decided to reinstall. whenever i formatted the drive AGAIN, i looked at the disk space information in the disk utility. it wasnt right. so i rebooted. upon booting to the jaguar cd, i ran disk utility again. this time it gave the proper information. i installed jaguar and a completely clean partition and havent had the problem since.
long story short. boot to cd, format, reboot to cd, install.