I'm posting my recent experiences with a trojan which I eventually magaged to remove (at least, that's my hope).
I am using McAfee Internet Security 11.6. A few days ago I mindless ran a suspicious program downloaded from the Internet which contained a trojan.
When I ran the program McAfee reported it as infected but evidently did NOT prevent the trojan to run and install itself (disappointing).
Since then the McAfee firewall started turning itself off every 10 minutes or so. I performed a full system scan with McAfee but the system was found clean.
Even when explicitly scanning (right-click on the file name, Scan) the original infected executable McAfee said it was clean.
I uploaded the executable to www.virustotal.com and here are the results:
I then downloaded and scanned my system (all files for each scan, it's taken ages!) with these programs (the latest versions available):
McAfee RootKit remover
Sophos Virus Removal Tool
SpyBot search and destroy
NONE of these programs found any infected file on my system, so this sucker of a trojan was hiding very well indeed!
I also tried scanning after rebooting windows in Safe mode (with or without network) but nothing changed.
As a last resort I physically took out the hard disk from my laptop and then used an external USB hard disk bay to access it from another computer and then scanned it using F-Prot security. This scan too didn't find anything; however I realised that several directories (including the directory where the original infected executable was) were not accessible from Explorer due to Window's privacy controls, so this scan probably doesn't really count.
Eventually I found threads on the McAfee forums reporting similar problems; in one of the messages there is a link to this guide http://malwaretips.com/Thread-How-to-completely-remove-ZeroAccess-Sirefef-rootki t-Removal-Guide "How to completely remove ZeroAccess/Sirefef rootkit". I followed the instruction to the letter and (I think!) I managed to get rid of the flipping trojan.
Essentially I downloaded and executed EZ_SireFix.exe, ServicesRepair.exe and ComboFix.exe (following the instructions) and having done that the problem with the McAfee firewall turning off stopped.
I downloaded and ran HitmanPro, and ESET online scanner and neither of them found any problem on my system (for what it's worth).
Over the following week I didn't notice any suspicious behaviours in my computer so I assume it is clean.