I struggled to get rid of the dll error however an alternative I found was to NOT use Custom Action and use the XML in the wix file to create the registry and then delete the key when uninstalling via the use of :
ForceDeleteOnUninstall="yes"
You have to use this in the
Example :
<!-- Register windows autostart registry -->
<Component Id="RegistryEntries" Guid="45C7AC46-1101-4301-83E1-D24392283A60">
<RegistryValue Type="string"
Name="FooStartup"
Value="[#FooMainApp]"
Root="HKLM"
Key="Software\Microsoft\Windows\CurrentVersion\Run"
Action="write"/>
</Component>
As found on : Registry change upon installing application C#
I really hope this helps someone new to WiX as it did to me.