I'm not quite clear on what you mean. The voltage ON the HDD circuit board is out of an expected value or the connector pins read incorrect?
If connector pins are off, unplug the drive and take another reading. I would've expected that if drive were pulling down the supply too much, it "should've" shut the supply down. Then again I don't recall the specifics of the supply you're currently using.
Are you still using that adaptable supply? If so, are you sure it's of high enough current rating? Most of the ones I"ve seen are 500mA, 1A at most which could be insufficient to spin up a drive, or in other words if it's non-regulated it might be pulling voltage down so low the logic is non-functional and needs then reset... but not by unplugging and replugging since the whole cycle repeats.
That is a good idea, probably the first thing I would've done.