I wasn't going to let it lie. ;)
The source of the bug was in SV_ClipMoveToEntity, where I had included the Q2 rotating bmodel code. It turns out that e3m3 somehow has an angles of 180, so clipping against the world in this case ran through the rotation code. The simple fix was to add && ent != sv.edicts to each test.
Lesson learned; even if something like this makes no sense at all, one should never assume that it's not actually set.
The good news however is that all I need to do now is finish up my PK3 loading and then I'm releasing!