I have not experienced this and don't know off the top of my head what might be causing it. Will you provide the exact steps you take (eg are you sending a "reboot to BIOS" command or are rebooting and then pressing F2 to get into BIOS?), tool(s) you're using (eg MS Config Manager OOB Console), and config info for AMT (eg TLS or/off, digest vs. kerberos, LAN or WLAN, etc).
Thanks for the response Jake...I didn't get a chance to trouble shoot again till last night. It looks like I have a bad motherboard I built a new system using a new mb and i5 660 cpu and it worked fine. I swapped out the cpu with the i5 650 from suspect system and it worked fine. Using the 660 cpu in the suspect motherboard resulted in the same loss of connection behavior.