Yeah that's fine. Sorry for misreading your post I think I've nailed the timing issues entirely with 0.1.6a. I have it running here with 7 characters for 2 hours. No timeout at all. You will also find it's faster because I tightened some of the wait states (they can be further tuned if everything is working fine for everyone).
A few notes on updating to a new version:
a) The "cookie.jar" file holds your session cookies (saved one-time code). So save that file if you don't want to do one-time code again.
b) "Queues" directory holds your queues. "Settings" holds your settings. Keep those and backup "Queues" in case we hit a bug with the queue planner. Will save you from remaking them. I have extensively tested the queue functions but at some point I'll start adding stuff and things can go wrong heh.
c) The contents of the "Cache" directory can be safely deleted at any time. It's HTML5 local storage/webicon database etc. (But not the directory itself. "Cache" has to exist. The code does not check for it and create it if it doesn't, yet. And Gateway fails without HTML5 Local Storage feature enabled).
d) Every other file should be deleted and replaced with the new versions. (Usually only APBUltimate.exe will be different but if I recompile Qt and Webkit to pickup bugfixes the libraries will change too. So play safe and replace them always).