I think it's a random problem.
For exemple, it's possible both tuners are busy, one by your channel stream (kodi) and second by epg grabber.
If the problem solved itseld, that's because when you just launched tvheadend, grabber absolutely wants update. After a few minutes, that's fine, and your tuners are released.
It's easy to verify, just restart tvh and test immediately 2 channels, on different frequencies. You can check subscribed streams (included grabber) in tvh status.
If it happens, try to disable initial grabber scan and modify crontab for it.