My girlfriend's son recently bought a Gateway 700GR with an ATI PCIExpress video card and running XP home for playing games. The motherboard also has an onboard graphics chip with its own port. He is using an older CRT monitor. On startup, no matter which port the monitor is plugged into, the computer sends the signal to the other port. I've gone into BIOS and set it for PCI(E) only, but it does not help. If he reboots soon after shut-down, the signal goes to the port it was using. If he waits 10 minutes or more, it goes to the other port. Since he wants the computer for playing games, he NEEDS the PCI(E) card as the onboard chip can't handle some of the games. I spent some time on the phone with Gateway support, but was unable to correct this. I'd appreciate any help (and so would he).

Open the Device Manager:
Start > Run > devmgmt.msc
Under Display Adapters you should see the 2 Devices.
Right click the on-board chip & choose Disable.

The problem occurs before windows starts.
Even when I go into setup (pressing F2 while booting) the computer sends the video signal to which ever port does not have the monitor plugged in.
I have tried booting with the monitor plugged in but not turned on and it still happens.

Are there any jumpers on the board that relate to the video?

anyway I found this post which is also what I had to do to change from board to card:
(S3 being board; V3 being card.)

"If you REMOVE the S3 from device manager it will be redetected on reboot and both the old and new cards will grab IRQs and memory addresses, leading to the conflicts that give you black screens. Remove the V3. Switch the S3 to standard VGA drivers and then DISABLE the onboard card in device manager.
Power down, install the V3 and reboot. This time the V3 will be detected and
prompt for drivers. The S3 will still show up in device manager, but with a
red slash to show it's disabled, hence not using an IRQ or memory addresses
to cause conflicts. One other thing that might make your life easier is to
load the proper drivers for the monitor by make and model, not just PnP or
SVGA, so the video card will know what refresh rates are supported.
Otherwise you risk having the new card select an "optimal" refresh rate that
the monitor doesn't support -- bingo, another black screen."

source

There are no video jumpers on the motherboard.

Your other suggestion seems to apply if the problem occurs after windows starts (I don't think that the device manager comes into play until windows is running). This problem is there even if I do a cold boot to straight set-up.

I will save this as a last resort. I might try it on my own computer, but I'm always a bit more reticent on someone else's machine. Esp. a 15 year-old who is a really great kid and who also uses this computer for his homework.