I've seen similar problems with a P3V4X knocking down the CPU speed during boot, but this only happened on rare occasions. The CPU reset has several possible causes, but the most likely is either over heating or voltage fluctuations. Here are some ideas, from easy to harder.
1) You could try reseting the whole system with jumpers instead of CMOS, but I don't think that will solve the problem.
2) You may need to update your VIA chipset drivers to at least version X.32. Check out the viahardware.com site. The 133A is a good chipset when you use the latest drivers.
3) The voltage to your SLOT 1 may be fluctuating causing the CPU to overheat. Check the voltage on your PSU motherboard leads. Maybe you can run ASUS probe to check for voltage fluctuations, but ASUS probe isn't known for stellar accuracy. I would trust a good VOM.
4) Early versions of the P3V4X have a WINBOND clock timer that's known to overheat. This is a well documented problem, and a Google search will get you tons of information on it. You might want to install a passive heat sink on the clock timer chip. Thermal epoxy would be the best method.
5) As a last resort, consider flashing the BIOS to 1.003. Frankly, I doubt if a new BIOS will solve the problem.
Obviously, when the BIOS doesn't detect your CD drive, that's a serious problem, but I don't think it's related to the CPU problem. I assume you have your CD drives running together on a separate IDE channel, and jumpers are set correctly. Does Device Manager see your CD drives or suggest anything unusual about your CD configuration?