You are right nobody that nobody did ask.
Since I was not using a custom ROM I had factory bootloaders.
I'm not sure what bootloader I had initially, but it did not have the CPLD-9 line. When I ran the RUU it upgraded the bootloader to SPL-2.07.0000.
No. My only rom update was to a stock rom. My real guess is a marginal connection somewhere in the phone. Since 9/10 times it boots into the bootloader and tends to get stuck there.