I just downloaded the AutoIt installer and editor from www.autoitscript.com . When I allowed the Avast anti-virus screen saver to run, it reported that 3 of the files installed from the AutoIt website to be “Win32:Rootkit-gen [RtK]”. Two of the files are installed from the editor and one of the files is from the AutoIt program. All of these appear to be false positives.
I should also point out that this was with the latest version of AutoIt and SCitE4AutoIt as well as the virus definition downloaded last night: 120118-0.
I just had a similar problem trying to run the AU3Info tool from within the SciTE editor. Avast complained about Autoit3wrapper being that rootkit mentioned above. Kind of a pain!