The +5V pins on the 44-pin IDE connector are in the same column:
If one were to connect the lower half of the cable to the upper pins, the problem is that five signal lines on the drive side would be tied to ground.
If one were to connect the upper half of the cable to the lower pins, the problem is that five signal lines on the host side would be tied to ground.
Other than those, it would just be wrong signals, using the same voltage levels and logic.
I don't know how these are implemented in hardware: should/could/would grounding the signal lines cause damage (to either side)? I dunno; me software-uncloid.
Shifting the connector by a single pin right (leaving the leftmost [bottommost in the image] pins not connected) is the most dangerous scenario, in my opinion, as then you'd short circuit +5V to ground. Depending on the motherboard and power supply, it might damage the tracks on the motherboard where pin 40 is connected to a ground plane; the short circuit current could be several amps.
Booting problems can be caused by faulty IDE-to-media adapters, or it could be a motherboard problem. No way to know, without testing. (That's why I suggested getting a cheap alternative adapter, like a cable-only adapter, to rule out problem sources one by one, in the other thread.)