I noticed a few odd things today.

[DirectorTsaarx]

I've seen the "shield residue" thing as well, but I think it usually disappears in the next combat turn, so you don't have to worry about carrying "conventional" weapons along with the shield skipping weapons. Of course, I don't build ships with only PPB's (or other shield-skipping weapons) and usually put at least a couple shield-depleters on my boarding party ships, so it's never been a concern for me...