So, nobody else has an idea?
At least it looks to me from the logs that hardware acceleration by OMXplayer is active.
The user @popcornmix advises in this current thread to NOT use this feature on Pis 2 and above.
On my Pi 2 model B unter Settings -> Player -> Videos -> processing the HW acc OMXplayer is deactivated and HW acc. MMAL active.
No idea whether this is really related to your issue.