>> What's the format and frame rate of the clips?
NA, seems to be doing it on everything, including non-video text clips, and through the preview before any encoding. Mostly though I use imported iPhone videos (H264, VFR, etc).
http://inaudible.co.uk/temp/videopad/intro.vpj
In the project, see the final clip when the fade starts (the others will do the same thing, but are on black screens when transitions start so you can't spot the added frames). But ultimately, just add a transition to any project's clips and watch. If it doesn't do it, it is just me :|
Here's an example export. It's subtle but you can see it - 0:25 before the fade, 0:47, 0:57, 1:07...
https://www.youtube.com/watch?v=VQlTKstkJkM
Note that the fades ins/outs of isolated text on seperate video tracks doesn't cause any issues, only transitions between clips in the same track.