What am I missing? Where is 'cron' involved in the Java code? Are you saying you are running the Java as the cron job via a script and that this then uses Runtime.exec() to invoke another script? What does the cron email show when the process does execute and those times when the cron job does not execute?
Note1 - your cron job will not execute on the hour since 0 is not in the set of times.
Note2 - your use of Runtime.exec() is flawed. You need to read the 4 sections of http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html and implement ALL the recommendations. Failure to do so will just cause you more grief.
Retired horse trader.
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