The cause: I was able to duplicate this reliably by the following method. Start up the PvE FTL character set, login. Open the ISBoxer in game UI, load "AutoHeals" repeater region. I have the repeater region on the right side of the window. When you mouse over into the repeater region, and then mouse over and click on a slave window, mouse repeater will be toggled on for all 5 windows. From here on out, mouse repeater seems to be randomly turned on when swapping windows. I'm sure there is a pattern to why, but I haven't figured it out. The only fix I've found is to completely logout and restart the character set. I did NOT try to just relaunch the character set, that may or may not fix it. I guess the problem is the repeater region being flush with the game window on the right side, so the mouse repeater is ON for 1 window due to the repeater region, but when you swap windows before that turns off (mouse out of the repeater region) it gets confused.
Ahhh, that would actually explain it. The Repeater Region doesn't know the mouse left it. It sounds like all you should have to do is go back to the offending window, move the cursor into the region,and then out of it (into the same window). I'll have to do something about this, thanks for the detailed information.