I'm having the SAME problems.  Just printed a 1040 with several schedule Es; when the client and preparer copies print, the FIRST forms that print are the 4562s and the Schedule E 2-yr comparatives.  Same with creating a .pdf file.  Very shoddy and unprofessional to send a client a .pdf with the form order all fowled up.

The same is true on 1120-S returns.  The FIRST thing that prints is an AMT depreciation report.

Please FIX this.  I've spent hours upon hours setting up the Print Order on how I want the returns to print, and yet, ProSeries doesn't follow my set up.