The Repository Type options are no longer available at study creation time, but they can be set via the "Manage Study" administration page. Once the module is enabled all the specimen repository admin options should appear on that page.

I'm puzzled by your comment about the Specimen module disabling itself. If this continues to be a problem (or you're still having problems getting your specimen repository configured) then I think we should schedule a screen sharing session to investigate.

Thanks,
Adam