My Intel D865PERL would always look to the SATA first and the IDE drives second. Once I performed a RAID 0 on two WD 250 gig Sata's, the SATA RAID 0 now acts like your SATA/IDE problem. If I put any IDE hd in IDE 0 (Primary) it tries to boot to the IDE. So, I'm with you on scratching my head on this one. I'll continue to do research and contact Intel and we can help each other out here. Sheesh!
Noli Nothis Permittere Te Terere!!
EVGA 680i, Dual EVGA 8800GT'S (650/950), 4 gigs OCZ DDR2 1066, Intel Q9450 at 3.8 Ghz, Koolance Water Cooled, Dual Plextor16x DL DVD+/-RW. Dual WD 250gb 16mb Cache Sata 3.0. 3DMark06 score = 19,168.