Well I feel like an idiot now. I finally figured out my problem....
As mentioned earlier, I have 4 MB controlled sata ports and 2 Marvell raid sata ports.... Even though I had the 4 set to IDE I had the Marvell on for my front panel usb, firewire, and esata. Ubuntu was reading the Marvel raid and assumed all my drives were raid. 3 weeks to find out it was a stupid on/off switch (so to speak) :P