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Thanks for the suggestions Paul. I actually managed to fix the problem, which was a sum of many little ones. I'm leaving some tips for anyone who might encounter this in the future:

  • One of the problems was the line TCCR5B = (1 << CS51); that should be TCCR5B |= (1 << CS51); I have no idea why this is a problem, since that register should be all zero except for the bit CS51.... but it works with the pipe, and doesn't work without it.
  • Another thing to take into account for people losing sync over time, is to make sure your baud rate matches the crystal you are running on your board/arduino. For arduinos with 16Mhz clock, running at 115200 is not a good idea, since this baud rate yields a 2.1% maximum error in the communication. Sadly, the rosserial_python won't accept custom baud rates like 250000 which yield no error. For more info consult this link: http://wormfood.net/avrbaudcalc.php.