Encoding subtites to a VFR mkv

[Fadeout4]

I'm trying to hardcode subtitles onto a VFR matroska video. Here's what I did step by step:

1) Extracted the timecodes file from the source video with MKVextract GUI
2) Timed the subtites in aegisub, then opened the timecodes file in aegisub and went to export > transform framerate, set the input to the video's VFRaC and the output to variable
3) Using megui, I encoded a .mp3 audio of the source video
4) Also using megui, I encoded the exported .ass file onto the video
5) Muxed the encoded video with the encoded audio, setting the video track to the timecodes file I extracted in step 1

When I did this, the resulting mkv plays with the video, audio and subtitles perfectly in sync. However, the end of the video is cut off. The length of my final product is 21:52, while the source video is 23:35. Why does it do this? The encoded video (before muxing) IS the correct length, it isn't until I mux with the timecodes file that it cuts off the end of the video.

[Bjs]

You might want to check the part about audio encoding ... the file is vfr ... if audio was encoder as other that could be the snag.

Extract video and that new mp3 as separate files ... use media info to confirm the following

1: Time lengths of all streams (should be exact .. some apps can choke)
2: Any differences between the original audio source and your new mp3 (frequency, bitrate should match or some apps will choke)

[Fadeout4]

Thanks for taking the time to help me solve this problem. Before I check the audio files though, I guess I should mention that I tried muxing the video with the audio WITHOUT setting the video track to the timecodes file just for the hell of it. While everything was out of sync, the length of the video was the full 23:35

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The audio file be it. I extracted the audio track from the original video and opened it in media info. They are both the same frequency and length (23:35). However for the bitrate it says:

Bit Rate Mode: Variable/Variable
Minimum Bit Rate: 8 625 bps

When I open the .mp3 I encoded, it says:

Overall Bit Rate Mode: Constant
Overall Bit Rate: 128 Kbps

I tried just muxing the encoded video with the .acc file i extracted from the source video, but that doesn't work either. I got the following error message:

Warning: AAC files may contain HE-AAC / AAC+ / SBR AAC audio. This can NOT be detected automatically. Therefore you have to specifiy '--aac-is-sbr 0' manually for this input file if the file actually contains SBR AAC. The file will be muxed in the WRONG way otherwise. Also read mkvmerge's documentation.

And the video still is in sync but cut off at 21:52