The Marvell IDE adapter on my mobo (ASUS p5q se/r, c2d E8500, 2x2g 800 RAM) takes over a minute to detect my IDE drive during boot up, and after looking around the net for some answers all I could come up with is "Ensure if the drive is on its own cable, that it is set to master", I checked that, and I already had master set... so I moved it to the end of the cable (no difference). Ive currently got 2x500g Western Digital SATA's, and my old 250g WD IDE, and ASUS DVD drive. They are all on their own cables, but I'm not sure how the mobo sees the IDE (it's also on its own cable attached to IDE port) SMART is enabled on the drives that support, and I don't think I have a BIOS option to turn it off.

Suggestions to try:

Contact Asus support.
Verify IDE drive and cable are good in another system, if possible.
Reduce IDE detect timeout in BIOS. The motherboard manual indicates 35 seconds is default. If the board waits 35 seconds detecting a nonexistent slave on the IDE hard drive's cable, that's a good chunk of your minute boot time there.
Disconnect all drives except for the IDE hard drive, disable the SATA controller in BIOS, and see if any boot time change is noticed. Then,
Disconnect all drives including the IDE hard drive and connect an IDE CD-Rom/DVD drive and see if any boot time change is noticed.