Steps to Reproduce:

Follow all the steps to generate a self-signed certificate as described in Running JIRA over SSL or HTTPS.

When you try to use the set the certificate path in the JIRA Configuration Tool the following is shown:

It's complaining about the lack of the Private Key, but the key is where it should be in the User's root directory:

laptop:~ pcora$ keytool -list -alias tomcat -keystore ~/.keystore 
Enter keystore password:  
tomcat, Nov 19, 2012, PrivateKeyEntry, 
Certificate fingerprint (MD5): 00:A0:94:5C:B7:BB:FD:D9:D1:BC:8D:46:03:80:5E:02

And also the trustedCertEntry:

laptop:~ pcora$ keytool -list -alias tomcat -keystore $JAVA_HOME/lib/security/cacerts 
Enter keystore password:  
tomcat, Nov 19, 2012, trustedCertEntry,
Certificate fingerprint (MD5): 00:A0:94:5C:B7:BB:FD:D9:D1:BC:8D:46:03:80:5E:02

Actual Results:
Using the JIRA Configuration Tool prevents you to properly configure SSL in JIRA.

Expected Results:

The user places the Key Store path and JIRA accepts it.

Workaround:

Follow the old way to configure, which is described in http://confluence.atlassian.com/display/JIRA051/Running+JIRA+over+SSL+or+HTTPS

OR

Generate key and import it to the keystore using one line command(to avoid exporting and importing):

keytool -genkey -alias <your_preferred_alias> -keyalg RSA -keystore <location_to_keystore>