So I had icon packager to change my icons before, now it does nothing, how do I change the icon theme now?

For some reason M$ included the code responsible for loading some of the customized icons in explorer. This means that IconPackager doesn't always work with alternate shells. Since M$ doesn't appear to document any of this there currently is no fix. The only option you have is to use a resource editor to modify the DLL(s). We're looking for a workaround, but it may take a while.