My problem turned out to be due to a part imported from Zemax, a ray tracing code. It's rays are just lines, with no solid volume, hence the problem converting to pdf. ProE has no problem with these files, but Alibre can't handle them. Alas.
I deleted the part from the design and it produced the pdf. Would be nice if Alibre could flag the errant part somehow. The "internal exception" message doesn't tell you where to start looking.