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.
The first couple versions of emphatic kept files open. v1.10 doesn't, and I had no problems syncing with it running (albeit not in the foreground state when I started the sync.) I don't run it from my music drive, though, and many people do, so maybe that's the difference.
Anyway, I would recommend using a ;@HOME/;@WORK tag instead of ;@AC/;@DC for those who think it's interfering with their syncs but still want to use it in AC mode.