I've been having an annoying issue with MTPuTTY on Windows 8.1 where when alt+tabbing out of the application, the first tap of alt+tab results in focus on MTPuTTY and not the next application like the shortcut usually behaves. This seems to only occur when a session is active.
This appears to be a known issue: https://github.com/jimradford/superputty/issues/216
It doesn't sound like their hopeful about fixing it soon unfortunately.
The last comment in the link suggests using autohotkeys to basically trigger two alt-tab commands instead of one when trying to tab and mtputty is open, which is a good solution if you regularly use autohotkey or don't mind adding it to your autostartup.
Yeah I know you asked this awhile ago and probably don't care any more, but any time I find an unanswered stack overflow question I wanted an answer for I try to go back and answer it after I figure out the solution to my problem.