When my link from the DS90UB635 is connected and running BIST I read registers 0x04 (DEVICE_STS) and 0x4D (RX_PORT_STS1) I can see the PASS, LOCK, PORT_PASS, and LOCK_STS bits are all set to 1.
When I probe pins 47 (PASS) and 48 (LOCK) they are both near 0V.
When I disconnect the link, the register bits all change to 0 and the pins are still 0V.
Is there a logical difference between the output pins and the register bits?
I am supplying 1.8V to VDDIO. The output pins measure 9kΩ to ground, so I do not believe they are shorted.