ISBoxer's standard Interact with Target mapping, which is generated by the Quick Setup Wizard, turns CTM on temporarily to perform the IWT, and then turns it back off. So if you were using the standard IWT, this is normal, expected and desired behavior. If you're not using it, perhaps you would consider it: http://isboxer.com/wiki/WoW:Quick_St...tion_with_NPCs

Otherwise, if you haven't removed the CTM On and Off mapped keys, CTM Off is bound -- in the game -- to CTRL+ALT+N. If you're hitting that or having ISBoxer hit it, that will turn CTM Off.

As far as the mouse centering issue, if you are clicking on one of those windows and not wanting it to move to the main window (e.g. having changed the Swap option from Always to something else), you should probably enable Focus Follows Mouse in your Window Layout. Alternatively, change the "When clicking to focus a game window" option, also in your Window Layout, to "Ignore the click".