MSI K8N Neo2 Platinum boot delay, missing SATA drive

For years I have been suffering through intermittent long (4-5 minute) boot delays during the windows loading splash screen. In many cases my system will boot without any delay. When the boot delay occurs, the splash screen stays dim for several minutes. There is clearly some time-out being waited for. If I wait for the boot to complete, I will nearly always find that one of my SATA drives does not show up. I figured the problem was a bad motherboard and I've had an RMA from MSI that I just haven't used - I didn't want to be without my computer for several weeks. I tried to buy one even from MSI, but they don't make them any more. Recently these motherboards have shown up on ebay and it took me several weeks, but I finally won an auction. I swapped motherboards and don't you know it, I still have this problem! To avoid loss of my SATA drives, once I see the delayed/dimmed windows splash screen I power-off-reboot. This may require several attempts (as many as 10) before the boot completes. I would greatly like to figure out what is going on and fix it.

My system info is:
2GHz Athlon-64
2x1gb RAM
nVidia 6800GT AGP
2x160GB Maxtor PATA drives
2x300GB WD SATA drives
floppy drive
Memorex DVD +/-RW

The installed nForce IDE drivers match the ones I find on the nVidia website (version 5.10.2600.446 dated 6/3/2004). I built this system December 2004. Linux boots without this problem - only Windows shows this as a problem.

Since the SATA drives often disappear after a delayed boot, I tried one at a time unplugging one of the two SATA drives and booting to see if one of the drives was causing a problem. It still had a slow boot problem even with the missing drive not connected. I also tried to disable the SATA in the BIOS, but it still had slow boot.

I have seen other (old) threads about boot delays, but I haven't seen anyone else reporting missing SATA drives if they wait for the slow boot to complete. I am almost to the point of upgrading to a completely new system to get beyond this boot issue, but I can see it will be difficult to migrate all of my hardware to any new motherboard, so it will be an expensive migration. I saw one suggestion to use bootvis to see where the delay is, but when I run it and reboot, it crashes after I log in.

Any suggestion will be greatly appreciated.

On a whim, I decided to try removing the nVidia IDE driver for the SATA port being used for my two SATA drives. I switched to the atapi.sys from Microsoft that is dated from back in 2001, but I've gone through 10+ reboots with no delays. I don't know if this totally resolves my problem, but so far it looks good. It is a little hard to believe that a 2001 generic driver could be better than a hardware specific driver from 2004, but hey, it seems to be working....

Although the boot delays seem to be resolved by switching to the MS atapi.sys driver, a couple of times I have booted to a very slow system. The drives are all there and task manager shows I am spending 98% of the time in idle even when trying to do something. It can take 10 to 20 seconds to recognize a mouse click. I suspect some hardware is generating a lot of interrupts that is causing the system to respond slowly. Is there any system log that can show what is making the system respond so slowly? It does seem to resolve itself by just re-booting, but it would be nice to know what is going on behind the scenes.