The scanning engine isn't always able to scan inside an installer. (If I'm understanding your problem correctly) So there could very well be a dangerous file packed inside and you wouldn't know it until you install the software.
However, you can submit the questionable file to
VirusTotal and see if all those other scanners agree that the file is harmful.
If it looks like a false positive detection, submit the file to
Comodo Malware Analysis and they'll fix it.