Interesting is that the audio breakups are not second long during playback but much shorter. Is this in line with possible issue with the frame counting algorithm?
No, the frame counting thing can be related to earlier termination than usual, but not cause an audio problem.
Anyway, when testing your sample, I recognized unusual error messages from the libav audio decoder.
It might be a problem related to a certain packing of the mpeg audio frames into pes packets
The other thing, which is possible are damaged time codes, but the reception seem to be good.
Another possibility are network problems, so that a buffer run out, due to a high data rate.
You can change the TCP receive window setting or improve the network connection.
Marten