Not sure how or why it reverted to the self signed certificate. I have limited experience with SSL certs and tomcat/apache. How do I specify and use my CA issued certificate?
Here's a doc I"m going to be using. Maybe it will help: http://www.solarwinds.com/documentation/WebHelpDesk/docs/WHDSSL.pdf
Did you make any changes to the original keystore file?
Once you add the ca reply to the self signed cert, it should turn into a trusted ssl cert. Best thing I can think of is that, you added the ca reply but did not save changes once you added it to the keystore.
What type of ca reply are you using?