The filemaker server admin panel is run as a java app, however I suspect there are still components of filemaker pro that require java to function. IE the web viewer, some of the ESS connectivity, etc..
More importantly, Keeping Java up to date is fairly important regardless as it's a pretty vulnerable thing to be using outdated versions of from a security standpoint. Is there an underlying reason why you don't want to install a java update?
Alan, if you have one our 360Works plugins installed, that will cause this prompt. Our plugins require Java, and since OS X 10.7 and later do not ship with Java pre-installed, they will automatically install it for you when software (such as ours) attempts to use Java.
Why does it prompt for Java SE 6 Runtime? When I Go to the Java Control Panel it updates to Java 7 Update 71 which is noted as a critical security update.
This is a bug in the handoff between Oracle and Apple that makes it a requirement to install Java 6 from Apple, even if Java 7 or later is available.
The Oracle bug report is here: http://bugs.java.com/bugdatabase/view_bug.do?bug_id=8024281