MeGUI thinks source is MKV so after encoding to MP4, it won't play back

[VideoFanatic]

Clip attached. When I try to encode an x264 1080i 25fps MP4 to an MP4 with MeGUI, MeGUI thinks the source is an MKV so I presume that's why the encoding won't play back?

MeGUI says in the encoding log that "total number of frames differs from the movie". I have FFMS source selected in MeGUI (so MeGUI generates that FFVideoSource line in script) and told MeGUI to encode to an MP4 yet for some reason the MP4 won't play back. I just encoded the exact same source videos last week without issue so I'm not sure what the issue is this time. The source is 25fps and after doing some remux edits I noticed that MediaInfo reports the framerate as 25.028 and variable when it's actually 25fps so I'm not sure if that's what's causing the issue when I then try to encode that file?

My script:

LoadPlugin("X:\Portable Installations\MeGUI 2828\tools\ffms\ffms2.dll")
FFVideoSource("E:\World Cup 2022 11 19 - 01 - LGBTQ Protesters at Qatar Embassay in London - England player says .mkv", fpsnum=25, fpsden=1, threads=1)
AssumeTFF() 
Yadif(mode=1, order=1)

[ProWo]

You source is 25.028fps (variable framerate).
Encode as 25fps.

Example below, encoded with clever FFmpeg-GUI, AVC, 25fps, CRF 23, Yadif Deinterlacer.

[VideoFanatic]

That doesn't really help mate. I'm trying to encode with MeGUI, not another program. Might give that program a try in the future though.

I AM encoding as 25fps, just doubled to 50fps. The problem is that MeGUI is changing the source file extension to MKV when it's an MP4.

When I set the source line as an MP4, Avisynth sees the video as 25fps. I previewed it in AvsPmod to test that.

[VideoFanatic]

If I remux the source file to an MKV and encode that in MeGUI then it encodes and plays back fine. Don't understand why FFVideoSource inside MeGUI reads the MP4 as an MKV?