Ok, I think I've found a decent piece to this puzzle.
The bot seems to get hung up whenever I've got a buy order or sell order that it's trying to adjust, that is a large amount above or below the regional average. It pops up the "this item is xx% above/below the regional average" warning window, and the bot doesn't know what to do. It clicks in between "ok" and "cancel" for a while, then closes the market out and starts again. My guess is that it continues to get to that point, dies, restarts, and repeats, never updating the orders beyond that one.
If you can figure out a way to get that fixed in the next release, I'll be happy to continue my subscription!
