Allow a Start-up Program to run unhindered

I have two programs that always result in a alert when I start Vista. One is
for a mouse and the other is for a PDF file converter. The only options on
the start-up pop-up are Close and Allow. I have tried to change the program
properties from Explorer and every time I change it, after rebooting it
reverts back. How can I fix this situation? I really don't want to turn off
the Access Control, but I would like to be able to boot up Vista and not get
the annoying pop-ups. I do like the pop-ups to ask if it is OK to run a
program, but I would like the option to tell it that the software is OK and
it remember that fact.

Any help will be greatly appreciated,
Benny