Just to add,
if any of the keys in application keystore have key passwords which are different from the keystore password then again you would see an initialization failure.
The recommended way to overwrite GlassFish keystores is to set the following properties inside domain.xml to correct values :
<jvm-options>-Djavax.net.ssl.keyStore=${com.sun.aas.instanceRoot}/config/keystore.jks</jvm-options>
<jvm-options>-Djavax.net.ssl.trustStore=${com.sun.aas.instanceRoot}/config/cacerts.jks</jvm-options>
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