Specific one I've seen aleks.com (math tutoring site). It still thinks Java needs to be enabled, though I've explicitly enabled it. But no website ever appears in the "Manage Websites" that use Java.
Is this something Apple with fix or should each website??
Fixed with Safari 6.0.5, that has site-specific Java whitelisting.
Nice that it also prompts you to update Java or else it will disable it again.
Further info: it works under Firefox 20.0, prompting me to run their jar
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