Hey,
It has to do with the MSbuild configuration that is being used in the WiX
project. Go to the "WixBuild.Common.targets" file in the root directory of
your Wix Source and add
<PropertyGroup>
<WIX_ROOT Condition="'$(WIX_ROOT)' == ''">D:\Other\wix3.5</WIX_ROOT>
</PropertyGroup>
at about line 35 (just after the CheckRequiredProperties comments), that
should resolve the broken assemblies problem you're having. It creates the
property (WIX_ROOT) that VS needs to fully evaluate the paths to
referenced assemblies if it's not set via a command line (like when you run
make.bat).
Stryder
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