Such a small application is not a big deal, correct. I'll see if I can write that over the course of the day.
Seeing an old mechanical harddrive in your computer, it may be that it's spin-up time knocks out the FPGA configuration, as the inrush current of a starting motor may put oscillation on the 5V rail. That said, ATX power supplies are far from recommended for Amiga computers, no matter how golden the promises are. PCs usually have point-of-load regulators being fed from the 12V rail, and hardly ever use the 5V rail at all.
Please see our PSU FAQ for details.