What permissions repairs? What's the message at the end? Is it: "permissions repair complete"?
Can you post a sampling of the output in that window please.
First, do you absolutely have to have Java? Unless it is required, I would not have it installed or at least disable it in your browser(s).
Next, have you tried to repair your disk? You do need to boot up from either your install disks or use Command + R or Command + Option + R (recovery mode) to get to that Disk Utility and then repair your disk.