Try to change the GUID of the components which are not uninstalling. I tried the same and it worked for me. It may be because the GUID is already registered in the registry by some other product.
The cause is generally messed up component reference count in the registry – often it happens on dev-boxes during development. Can also often happen to Installshield packages due to their use of the SharedDllRefCount concept (legacy, non-MSI reference counting).
Some technical details:
Change my component GUID in wix? Test on a clean virtual to verify the problem is real and not a dev-box issue. Changing component GUIDs can have repercussions (patching problems etc…).