Well now this is a triple post... but I guess there's reason for that. Anyways... I cleaned out the ball valve with hot soapy water then rinsed it very well. I greased the seal, and tested it (to avoid that being a variable). It sealed again. Then I opened it and vented the small volume of 1,000psi air I used to pressure-test, then checked it again. The leak was bigger. I'm currently in the process of cleaning it again. Also not the the leak is occurring in the last portion of the port to seal. The valve closes in the picture from right to left.
So here's my understanding of the situation: Blasting a lot of air past the seal has somehow eroded or pushed it out of its groove far enough that it does not seal anymore, until it is hydrated, in which case it deforms or softens and settles back such that it seals again. Until I blast air past it...
EDIT: Some more extensive testing has shown interesting results. Small leak on first pressure cycle (pressurizing from atmospheric to 1,000psi), no leak at all on the second cycle, a slightly larger leak on the third cycle, and when the valve was opened (I used the other ball valve to vent the system so as to avoid the air blast being a cause), it released a small blast of air, presumably trapped inside the "ball." On the fourth cycle the leak was much more significant, probably because I opened the valve previously.
Is there any way I can fix this? I know I can unscrew one side off it, but I'm not sure what that'd let me do.