Heh heh... Commence the "everybody yell at mudskipper" portion of this thread!! LOL (& sorry for the long post--I hope it makes sense)
First off, your best bet is to get an IDE cable that does not have any pins blanked out.
You will find some ATA33 drives with the pin out. Although I suppose that I don't actually recommend this to anybody else, this is what I do. ;-)
I take a paperclip, bend it out so that it has a bit of a straight part. Now I hold a lighter under the end of the straight side. Wait until it is good and hot. Now burn out the plastic blank in the IDE cable. It may take a few stabs, but it goes away and everything works just dandy--never had a problem with it. I have ONLY done this on ATA 33 cables, by the way. My guess is that it is there strickly to make sure that your cable orientation is correct. Perhaps it was a redundant ground??
Any way, yeah--pin one has to be lined up correctly on your laptop IDE especially. If you get it backwards, then you will apply power where there shouldn't be any. Bad thing. USUALLY the adapters are built so that, when put on properly, the sides line up with the sides of the laptop hard drive. If your adapter hangs past the edge of the hard drive, then USUALLY the adapter is on wrong.
Now--as long as the laptop hard drive is hooked correctly to the adapter, don't worry too much about the IDE cable from the motherboard being oriented backwards on the adapter. The worst that happens there is that the drive doesn't access until you fix it.
Definitely don't take my word as gospel here--triple check it before powering on! Mudskipper
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Groucho said it best- "A four year-old child could understand this! Quick! Run out and find me a four year-old child: I can't make heads nor tails out of this!"