[popcornmix]

Has anyone else noticed issues with the sound being sped up or slowed down when playback of MKV's first start? The Pi2 is connected to the Denon AVR and I have the Pi2 configured to decode and for 5.1 audio. After the first 15 seconds or so it's fine and audio is normal.

Yes, that is how dvdplayer works. When playback starts there is normally some offset in audio and video clocks (e.g. 50ms).
With "resample audio" that gets corrected by resampling the audio by a few percent. That does produce an initial pitch shift.
I have reported it to the dvdplayer guy (FernetMenta), but it's not an easy thing to fix.

If you change "resample audio" to "adjust pll" you won't have this effect (but some TVs/receivers may experience audio dropouts).
If you enable omxplayer in video/acceleration you won't have this effect.