I have Pi 2B, OpenElec and Kodi; Confluence skin.
I bought a licence for hardware mpeg 2 coding and I put the code into config.txt with my windows PC.
Is on the confluence skin visible whether mpeg hardware decoding is enabled and functions? I do not see any indication.

Is your data carrier a USB drive, formatted in NTFS? If so, your issue could be similar to the issue I had (strong audio distortion only in the first few seconds, whereas the video part played ok). After that, I formatted my USB drive in Ext4. Issue was gone. Transferring files from my Windows PC to...