Logged Feb 2015, AutoPIPE V8i 09.06.01.10:
In both AutoPIPE versions 09.06.00.19 and 09.06.01.10, when the "Scale Factor" for flanges is changed in the "View Settings" window/dialog box, valves are scaled but flanges are not. This effects both the view on the screen and (more importantly) DGN solid model export.
Answer:
This has been confirmed and logged under TFS-D177405: View Settings > Flange scale factor is not applying on flanges but valves. This will be fixed in a future version of the application.