You totally mix up different things.
1) imap and pop3 certificates have nothing to do with ispconfig. They are certificates of the pop3 and imap daemon. If you dont like the certificates that come with the linux distribution that you have choosen, then you might have to recreate them. The commands are mkimapdcert and mkpop3dcert. See: http://www.howtoforge.com/forums/sho...07&postcount=5
2) https access for phpmyadmin has nothing to do with ispconfig and is not configured with ispconfig. ISPConfig can be used to create ssl certificates for websites, but phpmyadmin is not part of a website that is created by ispconfig. So you get this error becaue you access a http service that is not configured by ISPConfig by using https.
If you want to use services from your linux distribution with https you will have to create ssl certificates manually for the host that you use to access it.