It was suggesting I ask this question in the video support forum so here goes:
Using Mediaportal PVR to record live tv. Running comskip to create the cut file. In Kodi 13 – 16 this configuration worked flawlessly using comskip’s .txt cut file. With 17 (all betas including 5) the player built into Kodi will begin the skip accurately but will either:
a. skip to a random point much later in the recording
or
b. shut the recording down and return to the listing menu.
I have tested both the .txt cut file and the .edl cut file created by comskip and with either the same behavior is observed.
To further test, when playing the same recordings using the same .txt or .edl file the skip is correct in Kodi 16.1
I have posted a debug log here: http://pastebin.com/3YFpsLb2
Any ideas on what I may have misconfigured or perhaps a bug?