One theory is that the newer versions of anti-virus software (avast for example) seems to have started checking what Mta:vc does to vice city.

When mta:vc starts, it injects memory into gta:vc telling it to use that mta:vc mission script and other scripts instead for the original. It injects the netcodes needed for chatbox, syncronisation, mission scripts etc. :rules:
As Mta:vc injects this the antivirus will check what mta:vc is doing, and as it thinks that mta:vc might be injecting malware into the game, and also that it's connecting tru your internet, it might think it's trying to establish a form of trojan connection, thus the antivirus disable it and label it trojan.

It sucks