Cluster Raspberry Pi power supply from an ATX PSU
According to the schematic posted on Raspberry PI stack exchange, an on-board 1.1A fuse exists between microUSB and GPIO 5v line. This fuse is 
not supposed to see current drawn from microUSB to connected USB devices. With your method of supplying 5v power to the PI, this fuse DOES PASS USB device current. It is rather difficult to determine in your complex power scheme (where multiple currents can flow in opposing directions) how much current a particular fuse will see. Fuses act on net current flow. Seems like this fuse is running at its limit, if your current measurements are accurate.
Your power supply is adequate, with Neil_UK's caveats about properly loading its other 12v and/or 3.3v rails.
The PI was meant to be powered through the microUSB - it should be powered from this point, else the on-board fuse may not properly fulfill its function.