Are you using OS3.5, OS3.9 or a 4GB aware device driver that supports TD64 or NSD?
If not (and this is a long shot), copying data onto partitions above the 4GB limit can corrupt data below the limit. That doesn't sound like your problem, but you never know.
There is also a PFS2 update patch on Aminet that fixes some bugs. If you haven't already done so, you might want to install this.
