No need to be gentle (but I will be) -- you have a very strange problem (TMK)!
You did the right things for resolution and starting up in runlevel 5. Do I understand correctly that the first boot after changing the setting in inittab
things worked correctly and with the second boot they did not? If so, try about 10 more reboots, checking the tty's, and see if you get the same result each time. Also, see if all of your tty's exhibit the same problem or just some.
To get more data, you could also try going back to runlevel 3 (I assume you have multiple tty's), manually start a GUI in one and while that is still running see if going to a different tty gives you trouble. If it does, try rebooting, starting up a GUI, shutting it down and seeing how the tty's behave.
You might also check the difference (if any) in results between a simple reboot and a complete powerdown.
I don't really have anything to suggest for a solution. I am just hoping that with enough data, maybe something will suggest itself. Sometimes it works. Sometimes it doesn't.