I was going to just edit my last post, but since I'm running a totally different version now (Dev 1.2.12) and wanted to say, that it appears the Sync bug is gone. After adding my XBMC host back to the app I went to Movies and was able to scan through all of them (it stuttered a bit, but that was while pulling in all the posters) after going through movies I was able to do the same with TV. For the hell of it I hit the "Home" button to see what the numbers were and the screen went black for a second before dumping me back to Springboard. I reopened the app and it's all running perfect now, the numbers all match, it's doing it's cycle for each category, etc.
I assume for Movies on the Home window it doesn't count movies that are inside Movie Sets which is fine but caught me off guard and I thought it was either an issue with my Library or the app until I noticed it matched the quantity when viewed (on XBMC) in a skin that didn't support sets.
Two biggest suggestions I have so far (maybe more later) is to change the "Watched" Status icon in Movies and TV Shows from that tiny white check mark to something else... or finding a way to place it farther over into the 'frame' of the Movie/Show. As you can see in the screenshot below, Eureka for example is Watched but you can't really see the check mark. The second suggestion is about Movie Sets, it shouldn't be too hard to make some kind of marking (or even the work 'set') appear to make it easier. I know the screenshot below is TV, but the sizing appeared the same as Movies, so I drew the box around Face Off to show there's a bit of room to play with for either/both of these requested markings, in fact, in the yellow part would be a good spot to center a tiny image of the word 'set' or some other fashion.
--Edit--
Turns out it doesn't handle Movie Sets yet anyway. Touching on a Set under Movies loads similar to a normal movie, just with all the information blank with no apparent way to view or select a movie inside the set.
--End Edit--
A note to those that have tried this App as is available in the AppStore: I'm not part of this project in any way but if you've tried that version and have an issue with it locking up, give them time for the new version to be released (it's more Apple's slow process to blame at this point than these guys) before writing a bad review. It was a simple mistake and these guys have been great working with people to get it fixed.