Not sure what's causing this for you, but two things to try out:
Firstly ... Xcode has historically had some bugs in this area that are only cured by quitting Xcode, deleting stuff from keychain, rebooting OS X (really - no idea what's in XCode that can survive an app restart, but I've seen it happen), and then restarting XCode. I haven't seen any of those for well over a year, but could be a regression bug?
Secondly ... although it doesn't handle certs, if you're not already you should be using iPhone Configuration Utility (http://support.apple.com/kb/dl851) for the provisioning profiles part if possible - it often provides manual fixes for Xcode bugs in this area.
Oh, thirdly (nobody expects the spanish inquisition): if you check Console, it sometimes contains extra debugging / error info for the commandline tools in Xcode that deal with certs and cert-signing (including error messages that appear nowhere else)