I though that the forum setting default option (in your forum Profile) was to notify users of new posts.
You can however, click the 'Notify' button at the top and bottom of the topic pages.
The Reputation services are to do with files being checked (are they known and in use by other avast users or whitelist, etc.) not the reputation of web sites. So yes I would enable Reputation Services.
Files with a low reputation are likely to be new, not digitally signed, in low usage, so even though they may not have been found to be infected/malicious, they are a little suspect.
Web sites considered infected (if that is what you mean by flagged) by the Web Shield will either have been detected by physical scanning of the content or listed in its malicious sites list. The Web Shield has a high detection rate with low false positives. Hacked sites (even ones you have visited regularly) are unbelievably common and possibly the highest means of infection. So shouldn't be treated lightly.
You can create a topic in the viruses and worms reporting the site you consider clean - ensuring the link isn't active (change http to hXXp) so it can't be clicked accidentally. People can do an analysis of the site and see if it really is infected or suspect.
If considered clean then you can report it as a false positive (e.g. first confirm) using the on-line contact form,
http://www.avast.com/contact-form.php?loadStyles for: * Sales inquiries; Technical issues; Website issues; Report false virus alert in file;
Report false virus alert on website, etc. etc.
