Converting a .m2ts containing VFR AVC into mp4/mkv

[GG-Xtreme]

I feel like an idiot when it comes to this stuff. After sorting out my other issues, I came across an odd video file: a 4GB, 1080p .m2ts that contained a variable-framerate H.264 stream and an AC3 track. The video plays fine in VLC (although seeking and time are completely broken, video appears as 00:00:00 in length and dragging the seek bar has no effect), and even plays fine in Windows Media Player (seeks fine and shows correct length).

I can't figure out how to turn this into a CFR mp4 or mkv. Every .m2ts converter I've tried seems to be looking for a large Bluray-format video stream and fails to load the file. Demuxing the .m2ts only gives me a raw .h264 file without timecodes or anything--useless, as I can only specify constant framerates when muxing.

I tried loading the .m2ts directly into MeGUI to convert to constant-framerate, and it loads fine...using DirectShowSource, which has been so-far useless to me, since the encoded files do not seek or play properly on Android phones or in MPC. Attempting to use FFmpegSource with the file just crashes MeGUI. Is there any other method of turning this .m2ts file into any constant-framerate format?