If this is the alert that you get when you try to run cmd, there is an intercept on the cmd.exe file to run this setuprs1.pif file instead.
Program & Tutorial - Also useful as a diagnostic tool -
FileHippo Download - HiJackThis and post the contents of the HJT log file here. - HJT Information
HiJackThis Tutorial.
Download and run HJT and post the contents of the log file (cut and paste) into this topic, you may need to split it over two or more posts depending on how large it is.
Do as Tech suggest on the boot-time scan, though I don't know if it would scan .pif files by default.
However, even if avast did move the setuprs1.pif file to the chest it wouldn't resolve the intercept on the cmd.exe file, hopefully HJT might be able to do something or we will have to find another tool to restore this function.