SATA controller failure?

Hello All,
I'm new to this forum and hope someone can help me with the following problem:
About one year ago I purchased a Dimension 4700 directly from Dell.
I bought a basic system and thus far added a second HD and two optical drives.
First thing that went was the on board sound card after about 2 months. I didn't bother using my 90 day warranty on this and bought a sound card that I installed successfuly.
About six months after buying the system, I started having problems booting the system up. Intermittantly, the system would fail to boot and give me the error massage: "no boot drive found"...trying to troubleshoot the system, I switched the SATA cables (I switched the ports, not the cables) between the two HD-drives and the system started to boot fine, but my secondary HD was not available anymore. So I concluded that the SATA conroller had failed.
I ended up buying a new motherboard, installed it and everything worked fine. Until about a week ago.  Same problem as above, same solution: Switching SATA ports allows me to boot and run the system but I again lost my secondary HD.
SO here are my questions:
1) Is this truely th SATA controller failing or am I missing something?
2) Is there a way to repair the controller or is the only solution a new motherboard?
3) If I want to buy a new motherboard, can I but something non-Dell that would fit in my Dimension 4700 case? Is that what is determined by the form factor? And what would fit (Intel, ASUS, etc.)
Any help is highly appreciated,
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Re: SATA controller failure?

A faulty drive is another possibility; have you tested it?

You can replace the onboard controller with a PCI SATA card.

No, nothing but another Dell board will fit this case without major rewiring, cutting and drilling of sheet metal.
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