No worries, it's a problem with the latest SWToR patch, and it's on our fix it list. I've been out all day (literally, out like a light

), but I'll work on it this evening.
Per the dailies, the bot has always had issues stopping mid-mission, depending on what commands AutoIt is implementing. However, between missions you should be able to close it and restart as needed.
The patch included a graphics update which is affecting image recognition while not in space. What we fixed earlier was the image recognition for reading the inventory credit total, but I'm working on the crew skills fix next.
@Dark and Bread: It's possible the SWToR graphics update (for shadows, not sure what else) is affecting performance on VMWare. Mine still seems to work, but I have no idea what the difference is between my VMWare/computer set up and yours.
