I have the same issue.. used a windows 2008 r2 IIS machine but get the signature message.. should work just fine.
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Make sure that you have MIME types defined for all of the various file types that are part of the repository. In particular, mine was missing the MIME type definition for .sign files (text/html). Also if you have request filtering of file name extensions, ensure that .json, .xml, .sign, .rpm, and .zip are added to the list of accepted file extensions.
Same here, MIME type .sign (text/html) was missing (Server2012R2). .json, .xml, rpm, and .zip were still part of the list of accepted file extensions.
you were correct, i was indeed missing the MIME type definition for .sign files. after i added it, i was able to update from my custom repository.
Sorry for the late reply