What kind of activation are talking about? MDS Activation or Enterprise Activation? MDS Activation is for users that want to download your published applications, whereas Enterprise Activation is to activate a user that you have added to the BES.
MDS Services is used when you want to publish applications that you have developed inhouse for your users to download to their BB.
The MDS Apache Tomcat is only for the MDS Services portion of the BES and does not affect Enterprise Activation.
Where are you trying to load the SSL Cert?
Have you checked the Event Viewer for errors or the BES logs?
The more detail you provide the better we can help.