In the end I had to go down the road of changing registry settings and getting the GPO to change this on log on, no easy way of doing it, thanks Mr Abode
If it's a setting in the options that you can address via manual intervention - then there are products out there that address those by integrating with GPOs (something like Policy Pak). Of course, may not work in your particular instance, but figured I would pass it along anyway.
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Using GPO to modify registry is always an option. I am using the Adobe Customization Wizard to create a custom deployment package with those settings included, and I really like it. You can DL the customization wizard here:
I used this walkthrough on my first go:
Getting this to work with PM is not difficult. Look here:
You can also download the adobe reader GPO admin templates here:
All in all, I tell my users to deal with the msg when it pops up, as it is in their own best interest.