From your issue description, could the issue be related to multiple JTAG source design is trying to access ATX PLL reconfig bus causing bus congestion and hence reconfig failure ?
You may want to review your reconfig bus connection again and make sure you are accessing the correct reconfig address space.
I would recommend you to start with sim verification for your actual design that doesn't use system console.
You can also refer to below example link to cross check with your own design
I am setting this case to closure since I never hear back from you after I provided some debug suggestion.
Hopefully you are making progress in your debug effort.
Feel free to file new forum post if you still have further enquiry in future.
did you find solution ?
if yes please share how it solved, as i am also facing same issue
3 different configuration but atx pll is giving single freq in output!
Please share the solution .