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UART problems when USB support is disabled

We're in the process of bringing up a new custom board running an 8168. When we finally got Linux up and running, the serial console got flooded by the following messages:

hub 1-0:1.0: over-current change on port 1
hub 2-0:1.0: over-current change on port 1
hub 1-0:1.0: over-current change on port 1
hub 2-0:1.0: over-current change on port 1
... 

The board does not have any USB ports (pins are connected per specifications) so we figured that removing USB support from the kernel config would fix the problem. Indeed the flood of messages went away, however, we noticed that the uart start experiencing problem. When USB is disabled, the console output is mostly fine, but the console input is unusable as we keep getting garbage characters. The board seems otherwise fine as we can telnet in and run various applications. The console is also fine at u-boot.

We ran the same kernel (with disabled USB) on the EVM and we don't see any issues with the console/uart. So there seems to be some HW problem, but I was hoping someone may be able to shed some light on the possible link between UART and USB.