Andrea, I think I might have confused the problem when your computer was acting strangely or when you reported the mkv slowness.  Anyway, from the information you provided and the dropbox transition.mp4, it looks like transitions are working as expected with your normal installation.  Thanks for checking, gg/pys

With my normal installation I have the following results:

https://www.dropbox.com/s/h8p4tyvx2snwiyi/transition.mp4?dl=0

I summarize the results:

mp4 --> wipe --> png --> dissolve --> 3gp/cut/3gp --> slide --> mp4
 30      29       29      21 (png?)    30  28  30       29       30 Fps

I can tell I don't have any particular problems.