Warning autorun changed pop up when I start portable apps - how to get rid of this nuisance?

Hi when I start my portable apps suite first thing that happens is that I get said pop up, the text is very long but it says that something changed in my autorun file and that may be because of a virus or something and if I did not do it myself I should scan the drive for malware bla bla.
The thing is that is nothing wrong with the drive is not infected with anything I has been scanned already I just want to get rid of the annoying popup without having to reinstall everything.
Any ideas? This is happening in W7, W8 it is not OS related.
Thanks