This is fixed in VisBuildDotNET.dll v6.2.0.4, which is in the latest v6.2 download and at
http://www.kinook.com/Download/VisBuildDotNET.zip (extract to your VisBuildPro6\System folder).
No, it will only increment once. The Make VS.NET action first builds/rebuilds, then increments and builds again only if the target executable changed.