in the bios change the setting for fast boot to normal (or whatever it is on the motherboards in question), this will give the computers a few seconds to "warm up", apart from that try the web sites of the Mobos, see if there are newer bios's available, you could flash the bios.
only do the bios flash as a last resort though.
see if anyone else can offer better advice, im sure they will.
I had a similar sounding situation. Does the CD-RW lights on the drive keep flashing?? This is what happened on my machine (twice). The computer seems to get in a loop of checking the drive, find nothing and so check again.
However on a warm boot up the drive checked itself twice and proceeded. Does this sound similar?
Just for the time being use the IDE1 for Hd and then IDE2 as CDRW drive alone both as masters..leaving the CDR unplugged/out of the picture ..If that clears the problem ..Move the drives physically around to accommodate the cables.