You may want to edit your original post to document what you found. It is a good lesson for people to see that these settings make a difference. Would hate to have people think the difference was caused by the powermeters and not by the computer settings.

done

Jack - so just to be clear...I should have the following set on both garmins correct?
auto zeroing ON
1 second recording

If I do those 2 things, the rest should ideally come within +-2-3% correct?

non zero averaging should be off
That doesn't count 0 watts when computing the average, you don't want that. With this change I would expect 2 to 3% agreement yep.

Auto-Zero should usually be on, this tells some power meters they may go ahead and auto zero themselves when they detect zero-torque. I think some power meters will ignore this, and some have issues with it on. With powertap, I would leave it on. With quaurq I'm not sure what effect it has. You may want to turn this off when using a trainer, as sometimes trainers don't play well with auto-zero features.

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yeah...typo on my part...i meant turn auto zero ON. I looked up the fenix3 manual and there is nowhere in the pdf that talks about auto zero anything in the entire document. if it uses another term, then I wouldn't know at this point. The rest should be the same settings. I'll be riding race wheels all week in prep for Sunday, but I'll test again the following week since my race setup is no longer powertap.

It is unlikely to be thermal drift.
1. the P2M adjusts for temperature, and I would let it and the hub autozero between intervals.
2. the results were repeatable.
3. the results after the battery change were repeatable.