Tvheadend

You use mkbmerge to remove the subtitle track. Which version of tvheadend do you use? And are you sure that your tv recordings are 24p?
I suspect that you need to recode your recordings before you can play them.

I have made a little progress.
I have been able to create a compatible video using mencoder, however, it seems to skip a frame each second. Maybe because I brought it down from 25fps to 24 fps? Although I assumed that when transcoding it should not create such artifacts.
On the other hand I have not been able to create something similar using mkvmerge, somehow even though ffmpeg -i tells me the video and audio is correct it will not play the file.
But is there a way to tell tvheadend which codec to use?
Or maybe it has something to with the container frame rate?

tvheadend just records the digital tv signal as it is received via the air/cable/sat. it does not alter the video and audio data. And because of that you can not tell tvheadend what codec to use.

So if you want to play these recording on your TV and your TV does not support the format of the broadcaster, then you need to recode them.

mkvmerge can only remove or add a datastream to an mkv file. It can not recode it. So if you want to recode then I think you have to extract the audio and video tracks, recode them with ffmpeg of other tools, and then merge them back into an mkv again.

Hein