The developer addressed that problem in an 3 Oct 2010 post (www.pdfsam.org); here it is:
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Hi everybody,
as some of you may already know by the forum, a couple of days ago McAfee antivirus reported an infection in the pdfsam-starter.exe. I’m sure it’s a false positive and I already reported it to McAfee attaching the sources of the pdfsam-starter hoping that they will fix this issue as soon as possible. In the meantime I released a patch containing a new pdfsam-starter.exe which fixes an issue on Windows 7 64bits (bug #3050730) and that McAfee likes more than the previous one. The patch can be found here, I also included the sources so anybody can check them or even compile the starter. I really hope to have a fast feedback from McAfee and I was also thinking about dropping the pdfsam-starter executable (that is the only Windows executable included in the package) in next releases, leaving there only the .bat script to avoid any further trouble with the wonderful world of Windows/Virus/AntiVirus.

Andrea
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I also used the firefox when I downloaded it but never got the notice about a malware. AVG also did not detect any problem with the file.

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Here are two work-arounds the developer gave on this issue:

1) by the way you don't need to use the executable but you can double click the jar file in the pdfsam directory (the exe file is there just for the windows start menu).
2) Anyway as simple workaround download the zip package, unzip it whereever you want, delete the pdfsam-starter.exe (since your AV will find it infected), start pdfsam running the run.bat in the "bin" subdirectory.