The handling of JCEKS keystores is broken in J2SDK1.4.2.
The first signs of the problem appeared in form of this error report. Instinctively, I suspected my own program, not the JDK. However, I couldn't reproduce the error with JDK1.4.1_05 but could easily do that with JDK1.4.2_02. And although the report mentioned only one instance of the problem, many of the JSTK utilities and programs that relied on a JCEKS keystore, failed. In fact, simple operations on JCEKS keystore using keytool, such as -genkey followed by -export, failed. In fact, the problem is acknowledged in a Java forum discussion as well.
As a workaround to this problem, I am making a maintenance release of JSTK, JSTK-1.0.1. This release allows a user to specify the keystore type as either JCEKS or JKS. Though the default remains JCEKS.