OK, here's an "update", of sorts and some more ill-founded conclusions :oops:
So, I got some new CD units in (the CD unit, not the motor part) and slapped one in the Duo with the most problems. This Duo had good Hu play and sound, but the CD drive was super problematic. Didn't load games well at all, lots of hanging, horrendous sound, you name it. Put in a new CD assembly and it works! Perfectly! No load issues. No sound issues. Perfect!!
So what does this mean.
Well, I still believe the problem is on the PCB. The main reason I believe is as larsulrik mentioned above, a transplanted CD unit
sometimes will work better in a DuoR than a regular Duo. Also, the sound issue is much more prevalent in a regular Duo than the R or RX. And one of the main differences in the systems (and there are few) is the capacitor type they use in them. The R and RX use mainly radial caps instead of surface mount and the rating seems higher.
One of my successful "revivals" of a seemingly sound issue Duo was taking a known working CD unit and putting it with a PCB that had bad redbook audio. The sound came back when I crossed in a couple of new capacitors during gameplay. After the sound came back, the system was fine and has been since WITHOUT leaving the new capacitor attached! Just leaving the old one in place.
What am I getting at?
Well, it seems that the problem is even illustrated with the above example of the fading in and out after years of storage. Sound fading and crackling is likely due to a capacitor issue. And the typical problem with a dead capacitor is it either dries out or loses charge. Capacitance is based on building charge between two plates and without it sound won't work right. So perhaps after years of storage the lost charge in the cap is restored with extended gameplay. And perhaps with extended gameplay (and resulting heating) the cap dries out a bit (if borderline to start with) and sound takes a shit.
So why does replacing the CD drive help?
Because that can be a problem in addition to the capacitor issue. If the lens needs to be tuned or is dirty, the system is going to have one HELL of a time playing properly and with such early CD technology you need all the help you can get.
So why does a drive work better in a R or RX and why are they more reliable?
I think the case is that the later (relative to the original Duo, not each other) R and RX models have better error correction on the board. That or the more robust caps help out with these. A drive that is out of tune and fails on a regular Duo may therefore work better on a R or RX.
So, all that said, I have a lot of work to do. I have TEN Duo systems on hand that have audio issues. TEN. That doesn't include the two from members here that are hoping for a fix! I hope to have more info on what does and doesn't work in the near future. Busy life doesn't make that testing any easier