RR itself doesn't try to minimize any embedded windows - ever. What it does is try to RESIZE the window to the area you specified for it to embed. The applications in question may be "overreacting" to the fact we're resizing them (when they wanted to run full screen) and this is causing them to stay minimized. Generally, if you want to run a full screen app, I wouldn't bother trying to embed them -- I would only make a button to launch them (And once they close you should be right back at RR).
The only way we could suggest more is if you tell us where we can get one of those apps (even if trial/etc) just to test/look at them.