I have a working 1.6.3, on Skyrim version 1.6.640, if you are using any newer version, it could be the source of the problem.
I went from Dirty Deeds 1.4.2 to 1.5.1 (which introduces MCM but the functions did not work) to 1.6.3 and now everything works fine.
you can download 1.5.1 here and check if it brings up the MCM, then try to upgrade to 1.6.3 and finally get a working MCM:
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make sure to backup your save before any attempt at downgrading/upgrading.