MMAL Skipped frame or judder every few seconds

This maybe as stupid ignorant question but is your debug environment based on OSMC? Since this is the OSMC forum I bet it is. Because I’m having the same issue but just when using OSMC on the RPi2. I’m just asking because the Kodi part is the same with both OS I guess but something with OSMC is causing this that OpenELEC doesn’t have.

Edit1: the stutter/drop is actually not visible in the CodecInfo but you can see it. Just as a clarification.
Edit2: I can indeed confirm that enabling OMX with OSMC removes the stutter (which I would actually describe as a hiccup in my case) on OSMC.

I’m using this test file: https://dl.dropboxusercontent.com/u/789850/PendelTest.mkv

I’m posting the log here when I’m done in a few minutes.

And here is the log playing the whole test file posted above: https://dl.dropboxusercontent.com/u/789850/OSMC_hiccup.txt

Another one with passthrough and sync playback to display (adjust PLL). One sutter at around 12 seconds into the file for example:
https://dl.dropboxusercontent.com/u/789850/OSMC_hiccup2.txt

Stuff used:
RPi2
latest OSMC build, MMAL
doesn’t matter if passthrough, adjust refresh rate etc is enabled or not. I always get this with OSMC on my Pi2.
I can post a log playing the same file on OpenELEC if that would help.
This is nothing new for me. The hiccup was actually the reason I switched to OpenELEC when I got my Pi2 5 month back or so.