I was actually going to ask about that earlier but I got caught up at work. I noticed in the script.dat that the queue to check for valid entities was still really long, meaning the initial check was still ongoing. If all is well, this check should only take a few seconds at most to complete. If the mod setting "New inventory checks per tick" is set too low though, this check can take a lot longer.
Try restoring your mod settings to the default values (from in-game):
Ticks between cycles: 3
Inventories per cycle: 10
Chests per cycle: 1
New inventory checks per tick: 100
This should make the startup check faster as well as improve performance in general. I'll probably take out some of those settings in the next update, since messing with them can cause major problems and the game doesn't seem to update the defaults when I update the mod. There are probably a lot of people having simliar issues.