Haven't done it myself, but a coleague reports that the Admin console gets broken.
See this thread for a possible solution: https://fmdev.filemaker.com/message/85266
Which specific Java Update are your describing? Do you mean the Apple Software Update issued 14 June 2012 for Java,
"Java for Mac OS X 10.6 Update 9 delivers improved security, reliability, and compatibility by updating Java SE 6 to 1.6.0_33."
-- Drew Tenenholz
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