I don’t know how far into my thread you dug, but on thing that helped me was setting up my gopro (could use a phone too) to slow-mo video the chain. I did it from the back to check alignment and then from the side to verify if it was the rear cassette or front chainring that was slipping. My gut said it was starting in the back, but then the video made it very clear it was the front. Anyway, helped me isolate the issue a bit more to have the video.
If you can get into LBS, that would help. My issue was just in the beginning of the covid panic, so I was 100% on my own.
I did see how you approached isolating the problem using your GoPro. After reading that, I did look down at the chainrings when I had the problem. But, yeah, I have an appointment at my LBS to do some other work on this “trainer queen” (bike), so I’ll ask him if he can try to help me with this trainer set-up problem. Honestly, I’m leaning toward the freehub suggestion - either worn pawls or ratchets. I’ll try not to bias the LBS mechanic, though … 
Thanks for following up.
I’m having a similar issue with a nasty crunch whenever I put torque through the pedals on the trainer (it’s fine outside). Also I tried my other bike on the trainer with the same result.
I’m also wondering if it has something to do with the freehub, but I took it off and cleaned it up, the pawls were moving freely, I put it back on and tightened it, but it’s still doing this:
I also have a KICKR 2017 model and experiencing chain skips/pops on intervals above 250 watts. I got in touch with very helpful Wahoo Customer support and they got me to do a factory spin down and some hardware tests first which didn’t resolve. Then was asked to remove and take photos of the freehub which has some damage to it. They’ve proposed I try a new freehub which I’m awaiting to see if that resolves the issue.
It has been since early this year when I first encountered the “skipping” drivetrain problem on my 2017 Kickr. I sure sounds like the freehub is slipping, but upon examination it appears that the pawls are fine, so you’d think the freehub wouldn’t be the problem. The belt was a tad loose, so we tightened it up after examining it for wear. No noticeable wear (I’d been using it since Dec '17 or Jan '18 during “indoor” season riding - Zwift, Rouvy, etc). So, I’ve probably got at least 5-6K miles on this device.
I finished this indoor season off on a dumb trainer, and occasionally hop on that trainer during bad weather days, so I’ve been in no hurry to get the Kickr fixed. But, I just recently ordered and received a replacement belt. Once, I’ve replaced the belt, I’ll see if that resolves the “slipping” issue. If not, I’ll order a new freehub.
I’d be interested to hear from you, @Marcus_Gaskell , to learn if replacing the freehub does the trick in your situation.
Ride on, all!
I’ve got this same issue on a 2018 KICKR. I have changed the casette and chain and tuned the drivetrain, to no avail.
I am guessing it is either the frame flexing or something to do with the free hub. I’m going to setup a camera to try to tell more. I’ll keep you all posted.
Did any of you ever figure out the cause?
One question I’d have is if this is an early sign of needing to replace chain rings? I was getting this on the road but only when under load. I ended up needing new chain rings.