Drives Added Via Expansion Cards Keep Disappearing

I'm not certain if this has anything to do with Windows, or my motherboard, or overloading my system, or whatever. But I could use some input.

I built my current system in the summer of 2009. I tried to "futureproof" as much as I could by putting in a Corei7 processor (the low-end, 2.66 Ghz one), an Intel 80 GB SSD boot drive, a 10,000 RPM WD Velociraptor secondary drive, 12 GB of DDR3 1666Mhz RAM which I later learned my Gigabyte GA EX58-UD5 Motherboard DID NOT want to run natively any faster than 1333 Mhz, a 2GB DDR5 ATI 4870 Sapphire video card, and a BD-write drive I already had I'd installed in a prior system, as well as a DVD-writer and a card reader/writer with additional built-in USB ports and an E-SATA port.

This particular motherboard came with 10 SATA 2 ports and 10 USB ports (not to mention more I got with the Coolermaster Haf 937 case I used and that card reader, plus a couple firewire ports (I LIKE lots of connectivity). I never used all my SATA2 ports, although quite a few were hooked up, what with the connections for the case and card reader (which has since bit the dust)...

Anyway, a year or two later, after SATA 3 and USB came out, Newegg had 600GB WD Velociraptor SATA3 drives on sale for LESS than I'd paid for my 300 GB SATA 2 drive, and since I largely used external drives for a lot of my storage, and those were becoming available in USB 3, I found an ASUS card (U3S6 -- PCI-E 4) that had two internal SATA 3 connectors and two external USB3 connectors, and away I went. (I also added an additional internal SATA 2 7200 Hitachi 2 TB drive as a primary file storage drive at that time, with the first SATA 3 external a 2 TB SATA 3 to use as backup.) Those drives all show up FINE when I boot up, but often after a few hours, or a day or two, they'll just "disappear" from my list of drives. I find this QUITE disconcerting, as the 80GB Intel SSD has proven too small, what with the 14 GB WinSXS is now taking up, and I just ordered a 256 GB SSD that comes with Acronis True Image from Newegg to clone it to -- and of course it's SATA3. As I didn't have any more SATA 3 slots left, I also ordered another SATA 3 card. The ONLY slot I had left was a PCI-E -1 slot, which it appears that card is designed for, but as this new drive will be my BOOT drive, with Windows and all my PROGRAMS running off it, I certainly don't need the system "losing IT" in the middle of a session! (Note, the SATA 2 Hitachi drive NEVER fails to show up. Neither do the 300 GB Velociraptor nor the 80 GB Intel SSD, which are all on the built-in SATA 2 BUS).

I've considered replacing this motherboard, as it's had some issues (BOTH of the two gigabit ethernet connections that came with it petered out, and I had to buy an add-on card to get my gigabit ethernet back (one WASTED PCI slot)! However, I've yet to find ANY other motherboards that have anywhere NEAR the connectivity this Gigabyte board came with. Or is that the problem? Did Gigabyte overload this board?

The other day I thought to update the BIOS on the board, and although it took two reboots, I haven't "lost" any of those drives since (been on, or in "Sleep" mode ever since), so maybe it needed a BIOS update. I also went into the BIOS "Intelligent Tweaker" and toned down any settings that warned might create an unstable system (I was already pretty conservative with those, but I went a bit more conservative).