DVB-S2 - TS file plays fine, jerky when muxed to MKV



I have a TS file that was recorded from a DVB-S2 stream by MediaPortal. It contains a ~9 Mbps 1440x1080i25 AVC video stream and a 192 kbps AC3 audio stream. This TS file plays fine using a number of splitters and decoders (LAV, ffdshow, MPC-HC, Haali).

I want to convert it to MKV in order to save disk space but so far I've been unsuccessful. I've been using MKVMerge and I've also tried running the TS file through TS Doctor before remuxing - either way, the resulting MKV file keeps playing in slow motion, then swiftly catching up, then playing in slow motion again. Since the problem exists with multiple splitters and decoders, and the slow motion bits are always in the same places, I can only assume there's some damage in the TS file or something?

Is there anything I can do to get this file working in an MKV container? I've attached a sample below in both formats:



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