Okay, I had a couple of hours free time this afternoon and worked on the prototype.
Mystery solved.
I found out it was two separate issues... and both issues were on the same channel!
One channel was kinda like "superchannel" and was immune from all these stupid problems. The other channel was like a problem child on crack. <shrug>
1. Because of my original error in drawing the schematic (and thus the error on the PCB design), and trying to jury-rig a solution, etc... etc... well... that kludge solution worked for the superchannel but it didn't work on the crack channel. Weird. Don't ask me... I don't know why. The 2nd problem channel doesn't have a reliable startup of it's phantom power. Sometimes there is PP, sometimes not.
So this time, I really fixed the wiring by doing it the way it's supposed to be in the schematics. YES! It now works reliably, and there is 48V phantom power reliably on both channels, everytime. The DC-DC converter sounds happy too (which was a clue for me), and the DC waveform on the oscilloscope looks way way much better.... the way I expected it.
2. POPPING SOUND. Another mystery that only happens on the crack channel. The DC-DC converter was just fine. As I said, it's not microphonics. And no need to hot-glue anything. Don't want that ugly stuff on my board.
The problem was the BurrBrown chip which I'm using as a DC servo. (yeah, my pre has no capacitor in the signal path between the mic preamp and the output driver... I'm using a DC servo). I guess this particular chip is marginal because as soon as I replaced it, everything was quiet and back to normal again. Tapping the board, and dropping it from 1 to 1.5" on the table was just fine. No loud popping sound, followed by some crackling noise. Sounds great!
So now, the prodigal son, errr... channel has come back to the fold and everything is working fine again.
I'll continue monitoring in the next few days to see if any new problem is discovered.
BTW.... running the pre on 5.0VDC input using the Tekkeon battery and with phantom power ON...and IT WORKS, my power-hungry FET condenser is happy and working. I'm very pleased with that.