Traxor, give some more specific details if you can
:
1) Initial shortcuts set for the bossprotection (the shortcuts you set for both accounts when you DID NOT use polygamy)
2) The correct status for both of your polygamised accounts. online? busy? away? is it personalised? before you enter boss-mode.
3) The status (also, is it personalised or not) to which your messenger should set you when activating the boss protection. Again, list them for the both accounts you're using.
4) also, check the other shortcuts of the other Plus! functions if they don't interfair (lock-mode) or even plugins...
When testing on my system with various polygamy patches (not that there are so many though, there are only a few places in memory/file where the actually patch could be done), both messengers minimized like they should.
But, there is something strange going on (at least here) when you SET the shortcuts and when you ARE using polygamy; Sometimes the shortcut that you set will not be saved properly for that account/msn messenger (and thus will not be used for that instance of msn messenger, which can give the result that you see).
You can test this easly by changing the shortcut (to something valid of course), pressing "ok", and re-open the preferences panel and look if the shortcut is still the same or if it has changed to "none". (all this when you are running in polygamy-mode of course)
the above happens randomly so it can't be realy reproduced. But once in a while, this happens.