This could have been as a result of having been infected by Gumblar, win32:Virut and or win32:Vitro which infect htm/html files inserting an iframe tag and this tag redirects/tries to run malicious programs.
If you are unable to use a text editor to find and edit these iframe tags (remove them) or don't have the knowledge to know if the iframe tag which may be legit or malicious then you could damage the file. So essentially without experience you could end up failing to clean these and if and when these are run your system could be reinfected. So you may be forced to add them to the chest, but if you are going to do a clean install of SP3 you might just as well save the data files you can't do without and start completely from scratch.
Also see, Automatic removal of Gumblar/Martuz trojan
http://www.danielansari.com/wordpress/2009/05/automatic-removal-of-gumblarmartuz-trojan/. Obviously this assumes the infecter was Gumblar.
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I don't believe this is a false positive:
You could also check a few of the offending/suspect file/s at:
VirusTotal - Multi engine on-line virus scanner and
report the findings here the URL in the Address bar of the VT results page. You can't do this with the file securely in the chest, you need to extract it to a temporary (not original) location first, see below.
Create a folder called Suspect in the C:\ drive, e.g. C:\Suspect. Now exclude that folder in the
Standard Shield, Customize, Advanced, Add, type (or copy and paste) C:\Suspect\* That will stop the standard shield scanning any file you put in that folder. You should now be able to export any file in the chest to this folder and upload it to VirusTotal without avast alerting.