The first power on is normal, reboot ls1046 fails to auto-negotiate to 100base-Tx mode
I believe that the mode you are referring is 1000base-KX and not 1000base-TX.
Does it mean, that you are connecting it to an external switch on 100base-KX?
If that is the case, then I would recommend disabling the auto-negotiation (AN) mode.
Additionally, on Linux, you have to use the "fixed link driver" whenever the auto-negotiation mode is disabled.