I obviously haven't seen the schematics for any of this, but from viewing the pixelnet hub picture in the wiki, it looks like there's no isolation diodes or jumpers between the outputs of the optional 5 and 3.3v regulators and the ATX connector.
Therefore, if you have the regulators loaded (as for the 12V only option) and plug in an ATX supply instead, you will have the ATX rails and the regulator outputs tied together, and the regulators don't like to sink current.
It's possible that I'm wrong here; we should wait for RJ to chime in.
/mike