Jim,
I applied the epoxy mostly with a squeege. I think what you described is exactly what happened. Oddly enough, I just received a newsletter from NewFound Woodworks with updates to their Fiberglassing DVD. One of the updates to the video was to explain the forming of the ripples. Their explanation was exactly as you stated.
Apparently, I did an Ok job removing the excess from the bottom to the bilge, but didn't get enough out from the bilge to the sheerline. That then later seeped down to the bilge, gathered, and formed the rippled areas.
This was a good discussion. Thanks for everyone's feedback.
Mike in Collegeville