@mediaman,
If, as I think you're saying, you use an LM317T to (try to) produce a +3.3V supply from a +5V supply from the Atola, then I suggest carefully measuring the +3.3V output. The LM317 isn't sold as an LDO regulator, and at 500mA, one manufacturer's version which I picked as an example (Fairchild) has approx 2V dropout (even greater dropout at higher current), and of course 5V (input) - 2V (dropout) does not equal 3.3V (output).
Therefore some of your problem
might be an out of tolerance supply to the drive, due to a possible +3.0V (or lower!) supply voltage. To detect any dips in that voltage (especially while the drive tries to spin-up), you'd need a 'scope - a DVM wouldn't be sufficient IMHO, due to its slow updating of the display.
Or choose an LDO regulator instead of the LM317. Or use the +12V supply from the Atola as the input supply to the LM317 (if the Atola allows that, and doesn't require a minimum load on the +5V rail - if it does require that, you may need to provide it artificially).
I don't own an Atola; my background is electronics, so those are just a few thoughts, in case you're chasing a power problem as well as (or instead of) a drive problem. Good luck
