That is indeed a bug in the validation logic of the Make VS.NET action. There are two ways to work around it for now:
1) Manually edit the .bld file in a text editor, removing the <FileVer> line of the Make VS.NET step (marked below):
...
<step action='Make VS.NET' type='0'>
<Attr type='11'>-1</Attr>
<Config>Release</Config>
<FileVer>-1</FileVer> <-- remove this line and save the file
<Filename>xyz.sln</Filename>
<ProdVer type='11'>-1</ProdVer>
<Version>1.2.3.4</Version>
<VersionSel type='3'>2</VersionSel>
<name>vsnet</name>
</step>
...
The step will then only set the Product Version when built. This would have to be done manually whenever the the Make VS.NET step is edited.
2) Use the field override capability of VisBuildPro to turn off the File Version option of the Make VS.NET step during the build (sample attached, also see 'field override' in the help index for a description of how that works).