Hi,
Thanks for your update. As I understand it, now you are observing two different problems:
1. RX parallel data not staying at constant
2. TX PLL no lock after reconfiguration
To facilitate debugging, we shall focus on the first problem first. I notice from your signaltap that the serial loopback enable = 0. I believe you are using external loopback from TX to RX.
Just to check with you on the following:
1. Have you had a chance to run Modelsim simulation with your test design to see if it is working fine?
2. Can you share with me a simple test design of yours? I would like to look into the Native PHY to understand your configuration.
3. In your test design, just wonder if you assert the serial loopback, do you still see the same observation where RX parallel data is not constant?
4 Just wonder if you have a chance to test with the previous simple test design shared by me?
Please let me know if there is any concern. Thank you.