Encryption may be good for securing data, but it blinds network-based IDSes. While there aren't any surefire fixes, these techniques will steer you in the right direction.
Encryption used to be unequivocally good for security. After all, it kept the bad guys from getting at our private information, right? Who could argue with that? Many of us became crypto-evangelists, demanding encryption everywhere.
Then we realized that we were blocking our view with all this encryption.
Administrators need to be able to look at the entire network to properly defend it. IDSes, IPSes, sniffer tools and network analyzers provide a clear view of network activity. But, the more prevalent encryption becomes, the more we lose that view.