I would revert back to a previous rockbox build and see if that fixes the problem. If not, then delete rockbox and then re-install fresh. The problem with rockbox is that they continuously release untested and unverified builds. It is kind of annoying to update daily and once you do, you realize that the new build has something that used to work right, no longer work right.
no problems running version 3 on a 32GB CF card DIYMOD 5.5G here never had any issues with skipping whatsoever. you might want to try defragging the drive rockbox should allow for that. in fact if you unmount it you should be able to do that in windows