I use psexec which has a problem when called from Java (or scripts). I found in sysinternals forum (http://forum.sysinternals.com/forum_posts.asp?TID=10825) recommendation to use remcom instead of psexec. I tried remcom and found that it fails in some cases connecting to admin$ with the following messages:
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Initiating Connection to Remote Service . . . Failed...
2007-06-05 09:36:00 UTC in Remote Command Executor