So we know the air source is apparently okay, and no leak, but the seal isn't getting air when the engine is running and tranny in drive, as designed. It inflates with everything off, so I reckon I'd suspect the brass regulator component and its wiring, which I'm thinking (but not sure) is the on/off air valve, since it has two wires emenating from it. I would think it shuts off air to the seal unless switched open by the tranny being in gear; alternatively, it must have been open when you tested the pump with ignition off, so without a schematic in front of me, I'm a bit befuddled as well. Tracing those wires through the harnesses would be no fun, even though each is supposed to have ID on them - it can be really hard to read.
If you have a multimeter and can see if the regulator valve is getting power as it should when the seal should be inflated, that would narrow things down; on the other hand, the valve must have been open for your puff test to have inflated the seal with engine off, so again, without the schematic I don't know how the electrical control of it works. Just be careful under there. Perhaps the voltage test could be made at the relay, which I guess I'd look for in the front electrical bay using the schematic and the "map" on the bay door? :-/ Also, does the pump get voltage when it should? Gotta be the pump or regulator voltage, I'd think.
Joel