Yeah I actually had the same problem off and on. At first I thought it was a voltage issue, So i tried ATX PSU, Sun PSU, and a generic PSU with 3.3VDC but it was all the same problem.
So I started changing out other parts and in my set up it seems that some of the JVS cause it to hang. I started with a Sega 838-13683-02 and it seemed to play Atomiswave games fine, but this is while I was testing everything and I was not happy with it. Then I switched to a Sega/Capcom JVS and it didn't work .. so I tried a different Sega/Capcom JVS and it worked. then I swapped between the different JVS to confirm my findings and yep its JVS sensitive it looks like. Just to make sure I went back and plugged in the Sega/Capcom JVS and tried all of the power supplies .. and WTF they all worked to play Atomiswave games.
So in my experience it's the JVS causing the Atomiswave NetBoot games to hang. Some people have found it was the power supply voltage.