What you describe is puzzling.
If what you describe is accurate it sounds like a bad cable to me. Maybe there is an intermittent problem with either the mic cables or the five pin breakout cable?
Do you have a multi-meter?
If so, check continuity on all of the cables you are using. I'd test the cables while jiggling them around, to make sure there isn't a short somewhere too.
If that's not the problem, then I'd check the voltage output of the PS-2 across Pins 1 and 2 and Pins 1 and 3. If the voltage is 48v +/- 4 volts then the phantom power is working. I've owned several PS-2's and I know they are built very well. I doubt it is the PS-2 itself, but I guess anything is possible.
Who did the 5 pin breakout cable mod? Maybe you could send to back to him to see if he can fix it for you?