So long as the players are numbered differently, or the setting is "AUTO," the players should link and talk to each-other without issue. The only time it really matters is when using the on-air feature of a DJM where you want to have the player number the same as the audio channel to which it's connected.
It doesn't matter which deck the USB is in, the other deck will use LINK, not the USB button to connect and read the device.
I would check the pins on the connectors and try a different ethernet cable.