unfortunately, the problem still with the UNUSED 3.3volt output, when used on an Amiga.
Some "cheap" ATX PSUs, when used on Amiga, gives unreliable output on the 5 volt rail (see at your 4.24 volt with Apollo installed).
Often (see at the ATX PSU specs) the 3.3 and 5 v power output, are given together (as total output Amperes)
When we use it on an Amiga, those ATX PSUs, works in an unbalanced way.
The solution, would be to use more reliable (more expensive ATX PSUs, with indipendently regulated output) or give to the PSU a "dummy" charge to the 3.3 volt output.
EDIT- erm . . . about how to achieve a reliable charge on the 3.3 volts line, any help wiil be apreciated :-)
A little personal note:
i own a PowerTower4000 (but its the same even on a PowerTower1200) with those little PCB with row leds-2 drive transistors and few polarization resistors).
Seen that i had the 3.3volt ATX output line there doing nothing, i have used it instead of the 5 volt to power the leds PCB (an easy way to dimm all those leds light).
Result . . . those very, very low power drain, from the 3.3volt ATX output, screws the whole PSU output (not so much but it does).