I've got the registered version of Trojan Hunter. It may well pick up things that A2 misses and vica versa. I don't use the real time protection of TH because it uses quite a bit of cpu every ten seconds as it checks the processes in memory. What I do like about it is that you can do a quick scan which takes about ten seconds.
I also have PestPatrol, including the Memory Check, which takes up next to nothing in terms of CPU. (Its a hobby of mine collecting all these programmes!) After the last two or three updates of PP, it has detected an "Unknown Trojan". This is a false alarm and may be what you are referring to. This so called unknown Trojan was actually deposited on my system at the exact same time as the PP update in a temporary file. Make of that what you will. PP is well known for false positives but it might just save my bacon one day.
Trojan Hunter is well thought of but unless, like me, you like collecting security programmes, I would think A2 would do the job pretty well and its free. (There is shortly to be a new beta available from A2).