I have the same problem and I was able to reproduce the issue.
It turns out reference aliases are ignored on projects containing xaml files which has an xmlns definition to the output assembly like xmlns:local='clr-namespace:TestProject'.
If you think this is your case as well, please vote up my bug report at Microsoft Connect.
EDIT:
There is a suggested workaround in the link above which requires editing the project file manually. In order for this to work, I had to give full path of the assembly. Add the following instructions to the end of your project file:
<Target Name="solveAliasProblem" >
<ItemGroup>
<ReferencePath Remove="FullPath.dll"/>
<ReferencePath Include="FullPath.dll">
<Aliases>ourAlias</Aliases>
</ReferencePath>
</ItemGroup>
</Target>
<PropertyGroup>
<CoreCompileDependsOn>solveAliasProblem;$(PrepareResourcesDependsOn)</CoreCompileDependsOn>
</PropertyGroup>
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