I am having the same problem!
Ever since I installed the latest update to Adobe Reader 10.1.3 (around the end of March) AR brings up the "Do you want to allow the following program to make changes..." whenever I open the reader. NO OTHER applications do this except those that really need this permission.
I have not changed any UACs and in reading Pat's suggestion on changing the UACs above, I would only want to make changes if they could apply only to the Adobe Reader program.
It seems to me that something in the recent update changed Reader to cause this alert.
I sure would like to get AR to run like it used to.
Thx for your help.