I opened a bug report to the effect that recording profiles were updated going from 1743 to 1777, and my selection "pass through" was replaced by matroska.
https://tvheadend.org/issues/2364
In the recording profiles (configuration-recordings-DVR profiles) you should be able to change your stream profile back to "pass."
I left it at mkv because I want to see how stable the mkv writer is these days. I am impressed, half a year ago it was impossible to write 2 mkv files simultaneously, now they work fine.