Visual Studio clean solution doesn't delete all dlls / project reference getting moved

Question

I have a VS 2008 C# web app with a bunch of project references to custom dlls. These are all at a relative path from the web project. Recently I've noticed that Clean Solution removes some, but not all, of the dlls from the web app's bin\debug folder. For example:

<Reference Include="TowerCo.Utilities, Version=1.0.0.0, Culture=neutral, processorArchitecture=MSIL">
  <SpecificVersion>False</SpecificVersion>
  <HintPath>..\..\Components\TowerCo.Utilities\bin\Debug\TowerCo.Utilities.dll</HintPath>
</Reference>
<Reference Include="TowerCo.WebControls, Version=1.0.0.0, Culture=neutral, processorArchitecture=MSIL">
  <SpecificVersion>False</SpecificVersion>
  <HintPath>..\..\Components\TowerCo.WebControls\bin\Debug\TowerCo.WebControls.dll</HintPath>
</Reference>

The first one works normally (clean cleans it, new versions copied to web project on rebuild) but the second does not. A side effect is that I don't automatically pick up changes to the dependency.

Thanks for any help.