Acrobat changes settings when saving to "printer box".

This is my first time ever posting (this is my last resort) and Im a bit worried that Im posting in the correct place, but here goes...

I have a Canon imageRunner 8595 and am using Acrobat 9 Pro. When printing a large multi-page PDF I change all my settings, 2 sided, long edge binding, collate, save in "printer box", etc, and the first print will be just fine. When I print it again from the saved file on the printer it will change settings, short edge binding (*which makes the backside upside down), group (instead of collate) or other settings will be changed. When I go back to Acrobat, I have not closed the document, the settings will be changed there as well. I can change them again to what I need and it just happens all over again.

I have talked to my printer technician and tech support at that company, theyve sent people out and cant figure it out. Then one guy tries printing a PDF from another program and it works just fine. It only does it from Acrobat. The thing is I have to use Acrobat because of the nifty print settings, namely one of the page scaling options.

Hope that makes sense... Im about to pull my hair out.