I was starting to use VirusTotal (nice tool by the way) and I would give you some hint how to interpret results (as you misinterpret it). VirusTotal uses one engine to check the file against many different antivirus tools. If during the checking it fails on some antivirus software it doesn't mean that the virus is inside. In case of BF2Setup indeed 2 of the AV software detect some problems (I have never hear about it before). But 62 other (with known names as Microsoft, Kaspersky, Symantec, McAfee) didn't found any problem.
Why those 2 has detected some problems? Because of they algorithm which is used to do heuristic (which in fact is guessinng). I do not know which algorithm is used for particular antivirus but I read on some dev forums some radiculitis rules like if code consist File.Exist method used it is marked as virus/malware/trojan/dangerous app.
The problem is that this is basic method which is used when you program application which uses files... in other case if file will not exist application crashes (you need to handle such cases in the code). If such rules are used that means that almost all programs will be treated as virus. And for such "antivirus" you have to be very skeptical.
So it is necessary to understand the result and use common sens when interpreting results of antivirus software.