1) WHAT popup?
2) Did you follow the bios flash instructions to the letter? If so, did it seem to complete properly?
3) Although bius upgrades are generally safe these days, if one DOES happen to go wrong it is possible to brick the system. We have to consider that possibility.
4) When you say you removed the cmos, I assume you mean you removed the battery. When you did that, did you also unplug the power to the computer? You must do both.
5) Does the system sound as though it is booting? If so, try a different display (also check the cable connections to the display on both ends).
6) Did anything else happen during the flash that you are not telling us? Did anything happen immediately after (you moved the computer, etc)?