DO NOT BUILD NEON BAYBUSES!!!!!!!!!!! I made one to control my 4 neons and it works fine. I booted into windows and flipped my blue and red neon off. BAM! BSOD! The immence power fluctuations brought my PC to its knees. I restart..."PRIMARY IDE DEVICE NOT FOUND" goody! Somehow I managed to get it working by putting it on slave. I dnno how but I just managed to fry its ability to be sat as master. Let this be a lesson to you. Learn from my mistake.
Sounds like a power surge. I always put large caps, and small filter caps on my homebrew circuits, just to absorbs RF and shocks. If it has high frequency (Inverter) I also use a Ferrite
Your problem (the power thing) is simple: don't connect your baybus on the same molex chain as your HDs. The sudden increase in current from your neons is pulling power away from your HDs, screwing them up. I've done this before a couple of times, but I never managed to actually screw up a HD, but I'm using CCs, not sure if that makes a difference though.
sinizter: sure. If you already know the power-on trick, then connect the neons or baybus (depending on your setup) into the spare PSU. You might wanna add a kill-switch for PSU #2 or else you'll still have everything on when your computer's off.
First if it is on the same power wire as your HD's I would move it. Then put two caps on each power rail. At least a 450uF 30volt cap to absorb large surges, (And provide current boosts when needed) And a 10uF 30volt cap to absorb general Hiss and noise. If you have a Iron Ferrite core (Round iron things) you can wrap the power cables around them, this will get rid of high frequency RF noise that can ride on the magnetic field around the power wires.