Any reason why my virus scanner just picked up a virus named Trojan horse Generic11.AMNM whilst installing Original Wars onto my brand new formatted machine? :(

what virus scanner do you use?

AVG 8.0 but admittedly it's the free version at the moment.

Ahh AVG seems to throw up alot of false positives, does it tell you the file in question that is infected with the virus?

Yep, it was the OwarDedicated.exe

My advise would be to scan that file with a couple other scanners just to make sure it isn't a trojan.
http://www.malwarebytes.org/ and http://www.kaspersky.com/virusscanner are both very good scanners and both are free to use.
scroll down the page a bit for kaspersky for the file scanner otherwise you will scan your entire computer.

Hmmm... Can't seem to unzip the file onto my computer without AVG popping up with the Trojan message and i'm not sure I wanna take the risk truth be told :p
Annoyingly I had downloaded and played Original War just over a week back and soon after my computer started acting odd/funny, which as I wasn't bothering to use a virus scanner at the time makes me wonder if the two things are connected.
Is there any way I can get the file scanned via the Kaspersky website without pulling it from the zip file?

If your computers been acting up anyway then maybe a full scan wouldn't hurt. It doesn't appear that you can scan without pulling it from the zip and the file scanners limited to 1mb which I wasn't aware of.
Malwarebytes is a decent scanner though, google it if you want the general opinion of other people.

Well like mentioned my computer was acting up a day or two after I got Original War and at the time I didn't have a Virus Scanner running but I formatted the machine yesterday and this is my first day back on the net so I made sure to get all my normal programs (Firefox, Open Office, Winrar/zip, etc. etc.) and with that got AVG in tow. Next were the games, so I downloaded all my Gog games, loaded up Steam, etc. and then began to install things. Everything was going dandy till I installed Original War and then bang AVG pops up just before the Original War set up finishes telling me this Trojan is sitting within the set up.
Is there a chance it could of been put in there by someone else? (Hacked a data base or something? I'm not hugely clued up on that area). I mean it seems odd to have a file that's labeled in such a direct way by AVG to the point where I find myself doubting the website and its security.

Only a Gog member could tell you if its been hacked and a trojan placed in the game, but technically it is possible I would think. I'll ask someone from gog to take a look at it.
For now though get a couple different virus scanners and give your computer or at the very least the file in question a scan and see what they have to say. If they all call it a trojan then it probably is, if its only AVG then it could be a false positive. AVG does have a reputation for false positives like I mentioned early.

From the supportsite
http://www.gog.com/en/support/original_war/Trojan_virus_detected_in_one_of_the_game_s_files
Problem / question
Trojan (virus) detected in one of the game's files
Solution
The game has a built-in IRC client, which some anti-virus programs interpret as being a trojan. Please do not be alarmed by this and do not quarantine nor delete this file.

Iv submited the 2 OW files that some AV's were wrongly labled as Trojans to a few of the AV's that allowed you to submit them False positives. General rule of thumb is that as long as the source is reliable (i.e GOG/OWSupport) then there is a very strong chance that its a false positive.

Under AVG ( free edtiion) even if I ignored the virus warning the program would still not launch - the exe being killed before it was allowed to run. To avoid this in AVG:
Tools - advanced settings - from the list under resident shield select exceptions.
Now in the new window click add path and find the original war folder and add it to the list.
AVG will no longer scan that section and you can run the game. The fact that its an identified fales positive as noted in the support section on GoG means that this is safe to do - its just the virus scanner thinking something is a virus when its not.
Note that other virus scanners will operate in a similar manner and have an exceptions list withing their menu system - usually hiding under advanced settings menus.

These are hits to "heuristic" algorithms:
http://en.wikipedia.org/wiki/Heuristic_algorithm
They have the advantage of being able to detect relatively complex patterns, as opposed to just matching a fixed list of "known bad guys." The disadvantage is that they tend to have significant false positives.
I get the same warning with Comodo. I really like using VirusTotal on these things; you upload the file in question, and the service tests it against dozens of anti virus programs:
http://www.virustotal.com/
When I uploaded the offending file, it was clear that it was just AVG and Comodo getting overly concerned, [url=www.virustotal.com/analisis/00631c197a5730d1da21080c8d3b49b4f187c1aa96963cf51159d82af9e75438-1253451736]39 other scanners found no problem with it[/url].