When you'd get the error messages that say frames are being skipped (like you did before), then you'd lose quality, because those frames are then missing from the feed, which can lead to visual stuttering. But when you say with NV12 now you only get the warnings, you wouldn't lose anything and in general it would be fine, though I'd still say something must be wrong, it's definitely not normal and if I was you I'd keep on investigating.
I agree that using JPEG there would be silly, with 1080p60 NV12 you should be able to go even without any compression at all, with that needing only ~1400 Mpbs (though Density at strength 1 can still be a good idea, surprisingly depending on the setup it can lead to lower CPU usage than not compressing, I think that's because it has very little resource usage while saving the network stack some work with data processing, which is also done by the CPU).
But just for the sake of testing, could you still try to enable JPEG, start with level 10, and if you don't get warnings lower the level bit by bit until you get them? So that we figure out which bandwidth is still working?
Could definitely be the case, did you try and increase send and receive buffers in the driver settings? Even on my 10G card the default settings for them were ridiculously low, I couldn't even reach 5G before I upped them myself.
Basically try and set a very high value (999999 or whatever), usually the dialog will then tell you what the maximum is and then you use that maximum. Example of such a setting:
View attachment 102599
Remember to do it for both receive and send (could also be called "transmit") buffers on both PCs. On my 10G cards (ASUS XG-C100C) it's set to 4096 for both now.