If you were running emphatic and you couldn't synch, that's a known problem that has nothing to do with the version of hijack or the version of emphatic.

The problem is because, if you leave emphatic running and try to synch, the player will be unable to remount the disk drives because emphatic is using the song files and the disk cannot be unlocked. To prevent this from happening, you must run emphatic in DC mode only.

Note that you have probably messed up your drives and they are now in need of a manual FSCK per the FAQ.