The shields are disabled but the underlying processes are there for when they are restarted normally as in the case of a pause/stop restart of the shields, they need the processes to restart, this avoids having to reboot (so the instance of running a malware cleaning tool isn't a normal situation).
However, there is no problem in running combofix in this condition as can be seen in the cleaning routines in the viruses and worms forum. That said combofix is a tool that should only be run under guidance of a malware removal specialist.
So if you want qualified help - Go to this topic
http://forum.avast.com/index.php?topic=53253.0 for information on Logs to assist in cleaning malware.
Use the information about getting and using the tools and attach the logs here, not in the LOGS topic.
Given this is your first post, it is best not to post offensive comments like this when seeking help, lest you look like those you malign.