If you're asking if position matters in soup playlists created by jEmplode, the answers is "sort of". It matters in that position should ultimately be equal to your sort order in a soup playlist. You definitely shouldn't change the order of tunes manually inside of a soup -- that's gonna cause problems.
Is 3-down the "unplaylisted tunes" playlist? Or maybe that's tunes in the root playlist. Position there wouldn't be automatically controlled by jEmplode unless you set a sort order on Root (can you do this even? I'm not sure).
As far as the timeout on retries thing, someone else mentioned this too. It's kind of problematic, because if your Empeg decides to do a rebuild, that is totally dependent on the number of tracks you have on your player, so that could take 30 seconds or it could take 20 minutes. It's really hard to come up with a meaningful timeout. Now if someone wants to do the legwork of determining what the equation is for rebuild time as a function of number of tracks, then I could probably work that in there somehow to make it a little smarter.
For the rebuild thing, a sync failure is a case where I can't rebulid on the PC because the Empeg is in an unknown state relative to the in-memory database, so I have to fall back to an Empeg rebuild there. I can only rebuild the database in-memory when it's a succesful sync, because then jEmplode's view of the database matches the Empeg's view of the database. If the Empeg just died somewhere in the middle, jEmplode can't necessarily know in every case what the Empeg ultimately decided to keep vs toss.