I don't know exactly what changed from the first run of 50 to the next production. I know there was a muting circuit change, and a layout change probably to ease the assembly. Aside from that, I don't know of any differences that would affect the sound until the introduction of the new caps recently. Dan would know of course.
These were not the prototypes, though. The prototypes were the 2 box beta models. There is one here which you've no doubt seen.