I didn't notice at first, but this issue was fixed in commit 8eece74e on the master branch (thanks, Piotr!). So everything should just work on beta again. I built my own kernel from master not too long ago and everything is working fine.
I think I had a double issue. I have a realtek card from the same family in the desktop I am testing. I think my desktop needs the https://github.com/igorpecovnik/realtek-r8152-linux patch.
For now, I've switched cables around so I can use the 2.5Gps port at 100MBps at our home lan, and the 1Gps port directly into my motherboard port. The 2.5G card in the desktop is a pcie card.
I'll keep it this way until the TX checksum offload issue is resolved. Thanks for your help.