Everytime I download anything I always run the Avast scan on the rar file and then after unraring it I run the scan on the folder and a few times I have run my trojan scanner and there was a Avast trojan warning that pops up on a program that I scanned twice with Avast both in rar and folder before installing it.
Do you mean that scanning the unpacked files detect a virus and scanning the rar archive does not?
Can you submit it to VirusTotal and let us know the result?
More importantly, what is the malware name, the infected file name, where was it found e.g. (malware name, C:\windows\system32\infected-file-name.xxx) ?
Check the avast! Log Viewer (right click the avast ‘a’ icon), Warning section, this contains information on all avast detections.
It may be that your trojan scanner unpacks its signatures to scan and these are detected, this is speculation on my part as i don’t know what scanner you used or the file name of the detected file (above questions).