A quick update to this: I found that the problem appears to go away if I use a post script driver instead of the standard PCL driver for the printer. This doesn't solve the problem of e-mailing files out to clients and having them not print, however.
This may be a whole different round of questions, but how are fonts handled differently in PS vs PCL drivers? I wouldn't think the the file would be so dependent on the type of printer driver, but printing with the same driver from Word/Excel/Visio etc. vs. printing from Acrobat have two totally different outcomes.