Thanks guys. I'm done with this particular video now, but for the next one I'll definitely set things up with common frame rate and size, even if it means re-encoding with the quality loss and all. Hopefully that improves things.
As for Reaper resizing the video, yes, it resizes the video window when this window is undocked, but not when it is docked. When displaying the video in the docked video window, the size is fixed for all the different video sippets.
And I'll be sure to use DuckDuckGo next time I "google"