If you run the debugger in Eclipse, it will use the Java certificate store for verifying the chain of trust of certificates. I had a problem where the Eclipse debugger wouldn't connect to a server whose certificate was signed by my CA, even though OS X trusted the CA in Keychain. Turns out you have to add it to the cacerts file in the Java folder using command line. Check it:
http://blog.alwold.com/2011/06/30/how-to-trust-a-certificate-in-java-on-mac-os-x/
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