While I was working on a sub-app-based application earlier, I noticed that opening a dropdown menu or dialog box (I found this out when I opened the About box) would cause the framerate of a sub-app to drop even after the dialog was closed. I know menus will drop the framerate while they're open, but it normally reverts once they're closed. This seems to only happen if MIS is enabled. Sometimes it will fix itself, but more often than not it won't. Turning off MIS mostly solves it, as dialogs and menus won't cause this problem (as far as I know), but tooltips and similar can still trigger it. Here's a recreation of what I mean:
The first part is easy, just enable MIS and open/close the about box, and the framerate will drop (the counter won't reflect it, but it's noticeable). It may or may not fix itself eventually; it usually doesn't for me.
It's a little more subtle with MIS off. Hover over the Run button until "Run application" appears, then run it immediately. There's a good chance that the framerate will hang around the mid- to low-40's. But my application is a lot more complex, so it'll end up dropping down to 30-ish. The only way to really fix this is to restart the app if it happens, which runs the risk of it happening again if the file information pop-up appears.
This happens in both the .exe and .mfa files, in my experience.
I know sub-apps are extremely intolerant when it comes to having a different framerate than their parent frames, but there should be some way of forcing them to "re-sync" with the parent frame. I've tried setting the framerate in all my frames to the same amount at Start of Frame, but obviously that causes problems itself.