Relax, Mikey. Troubleshooting is a process, not a miracle.
I'm assuming you've tried some basic things like rebooting the machine, turning the computer completely off and turning it on with the 2nd external display already plugged in, trying the opposite: plugging in the display once the computer is already booted. You've logged in as a new user account to verify that the problem occurs in more accounts than just the one you use regularly, correct? Have you booted the Mac into safe mode to see if the problem manifests there? It would be helpful to know if the problem occurs in all those instances.
I'm also assuming that since you're familiar with the key combination for the universal access setting, you've tried some more advanced things. Your signature doesn't say what version of the Mac Pro you're running. If PPC, you've obviously booted in openfirmware and reset the NVRAM, correct? You've reset the PRAM as well, whether your Mac is PowerPC or Intel, correct?
Thirdly, it would be helpful to know what processes are running on your Mac. You're running a high end machine. Do you have any professional color-calibration software or anything of that nature running?
Finally, what preference files have you deleted in order to try to fix the problem?
