The person in question may need to update to 10.6.8 or 10.7.3 or later and apply the Flashback patch.
The program in question may need to be updated to deal with the Flashback patch. 10.7.0, 10.7.1, and 10.7.2 are not protected from the Malware and Apple's recommended procedure for those with 10.5.7 or earlier, 10.6 to 10.6.7, or 10.7.0, 10.7.1, 10.7.2 without the ability to update due to applications not being compatible with 10.5.8, 10.6.8, or 10.7.3 or later, is to disable Java. Sadly this leaves many Java applications in a lurch with a need to work around the auto-execution bug that the Flashback malware has created.
Does anyone have the slightest idea what could be causing this?
From reading through the entire thread in that forum, it seems most likely that some Java support file on that specific Mac Pro was corrupted (since others were reporting no significant differences between Lion & Snow Leopard). The OP "fixed" the problem by adding a Java 1.5 package. Reinstalling the current 1.6 package probably would have done the same thing.