Does not shutdown properly with new PSU!!!

I Just bought a New Antec NSK 4480B Case with a Antec 380 Earthwatts PSU and now when I shutdown, the only way to get my computer to boot is to clear the CMOS! I Really like the case and donot want to return it, but if the power supply is not compatible, then I might have to get rid of it.

I was wondering since this is a Older model board, then maybe the Power supply that came with this case is not compatible with the Motherboard. This board was one that had a 5volt lead on it, and was thinking that kept stored power for power up. Since the newer style Power Supplies delete the 5volt lead, then the only way to power up is to clear the CMOS and reset the Bios. I don't want to keep the computer on all the time, since the last computer I had fried the Motherboard due to overheating and lack of sufficiant power, (Emachines W2040, need I say more).

yes, specs are in the sig. I have it set for the setting S1 & S3 (STR), I do not have it set forany wake-up features. the only thing I have set different is the Chipset settings, and have disabled the 3.4" floppy drive.

The chipset settings I changed was aperature to 64 MB and the next one to 128 MB, can't remember what it is. My brothers computer did the same thing when we first put it together, but it was fixed when we put 2 switches on it instead of the single push button. It's a Frankenstien 98 HP with a 2003 HP Asus A7N8X-LA, that he insisted on having a 3" toggle switch on the front. Once the toggle switch had a secondary push button switch installed, the problem stopped. Am I going to have to do the same thing to get this one to work?