I had problems as this when i was installing certificates first time. And acctually sometimes still have :-)
One problem i run to was that i sometimes acidently used different JVM:s when importing the keys and when reading them with glassfish. This happened because the user i had importing the keys had different JAVA_HOME defined.
Other problem i have been having is that when the passwords are changed and other than the default changeit. One way could be to change the master password for glassfish and see what happens. See this URL:
http://weblogs.java.net/blog/2007/11/19/ssl-and-crl-checking-glassfish-v2
These are two issues i have been having trouble with anyway, might help you as well :-)
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