Wix visual studio project (msi) building with wrong name

This is hard to answer without seeing your wixproj file.
Most likely you set the OutputName too early in your targets execution path.

What would definitely work is (Wix5):

<Target Name="SetOutputFileName" BeforeTargets="AssignTargetPaths">
<PropertyGroup>
  <TargetName>Yourname$(Platform)</TargetName>
  <TargetFileName>$(TargetName)$(TargetExt)</TargetFileName>
  <TargetPath>$(TargetDir)$(TargetFileName)</TargetPath>
</PropertyGroup>
</Target>

or (Wix3x)

<Target Name="SetOutputFileName" BeforeTargets="BeforeBuild">
<PropertyGroup>
  <TargetName>Yourname$(Platform)$(TargetExt)</TargetName>
</PropertyGroup>
</Target>