I'm having the same problem and installed MissionControl version 1.6.3 from the start. Blacklist does not work on any 3rd Party component for me on Joomla 1.7 and I've been looking for an answer. I did test the Blacklist on Banners and it also appeared not to work. However when I refreshed the page, it loaded the selected template from the Blacklist. Navigating to AcyMailing from Banners, it too then is recognizing the Blacklist template. Unfortunately if I navigate back to a component not Blacklisted and go back to AcyMailing the Blacklist functionality no longer works again. Refreshing the page on 3rd Party components also does not work.
I posted this issue in another similar thread that has gotten ignored.
While I realize this is a free template, I'm a paying member and would like to know someone is working to resolve these issues. AcyMailing is a major component and it does not work with MissionControl. I need to Blacklist it or hopefully some day soon update MissionControl to support the component.
I haven't checked in a few weeks, but I had this same issue, with 1.6 and 1.7 sites. I had to bail on MC because of it. It doesn't play nice with CiviCRM so I was hoping to blacklist it, and it just never shuts off even with the black list enabled.