I wanted to post this time ago, but it's never too late.
I notice that, in MM, windows and 'sub-windows' have not that kind of priority they shoud have. For example, in the 'options' window you usually open new windows or dialogs to configure some plugins, etc... It's extremely easy that this sub-windows (if this name exists) or dialogs 'disappear' if you click, let's say, somewhere out of the dialog itself. But they don't really disappear, they just go behind all the opened windows. So, since these dialogs have no notice in the taskbar, unless you know what's happening you would think that MM is dead cause you cannot interact with it while other dialogs are opened (and they are, in the bottom). When you finally close MM (from the tray icon) you realize what was 'freezing' MM, seeing the small dialog popping up and closing together with MM.
And also if you knew what was going on, it's not pretty to go and look for that lost dialog.
Without further ado, please set windows and dialogs to be always on top, when the MM window is on focus.

Have a good day.