I had a similar problem at some point.
Apparently the Linux nvidia driver, when it sees a TV is connected, then it defaults
the output to the TV out only.
I would reboot all the time, and once X loaded, i would loose signal in my CRT monitor,
it took me a few weeks to figure out that the nvidia driver would default to the TV out
port when the TV was connected.
I solved it by defining "DFP" (for digital flat panel) in the XF86Config.
Maybe you have a similar problem?