The solution is to apply IntelliLock signing before the main build. The solution is the same as in this question.
<Target Name="AfterCompile">
<Exec Command="$(IntelliLockLocation) -project $(IntelliLockProject) -file "$(ProjectDir)$(IntermediateOutputPath)$(TargetFileName)" -targetfile "$(ProjectDir)$(IntermediateOutputPath)$(TargetFileName)" -snkeypair "$(ProjectDir)$(AssemblyOriginatorKeyFile)" -snpassword *****" />
</Target>