I haven't contacted Schiit yet, however, I have been facing the same issue since day 1 with a set of perfectly matched pair 6N1P tubes. Relative to the tubes that came with the Valhalla 3, my matched pair tubes produce a much more enjoyable sound to listen to. However, the amp enters protection mode pretty frequently after 15-30 minutes of use...
There was another person who commented on this issue in this thread (post #539), and they found that connecting the amp directly to an outlet resolved the problem for them. They had it connected to a surge protector previously, which was the culprit to the protection mode issue that we are all facing. And mine is also connected to a surge protector and cannot reach an open outlet.... But today I will be receiving a 10ft power cord with the same specs as the default power cord that will be able to reach a separate outlet. So, I will update this comment or will post a new comment if this resolves the issue for me as well.
Ultimately, I really hope this does resolve the issue....as I had zero issues with compatible tube rolling on my Valhalla 2 connected to the same surge protector. Additionally, I have sets of matched pair JJ ECC88-Gs and Gold Lion 6922s coming in the mail within the next month! And I really hope that I can compare them and enjoy them without any issues.
Edit - Also, it always takes exactly 60 seconds for my amp to start playing audio after being turned on, regardless of which tubes are installed... But Schiit-Talker says that audio output should start within 15-20 seconds after powering on the Valhalla 3....so perhaps there is an issue with my unit...or perhaps the surge protector is causing this delay as well. I should hopefully have the time to find out if this is the case tonight and will keep you guys updated.