What is the deal with Java and permissions on 10.6.x?

[AllGold]

For quite some time on Snow Leopard I have been seeing tons of permissions errors with Java every time I run Repair Permissions. Disk Utility says it fixes them but of course if you immediately run another Repair Permissions you get the same messages.

These are not just informational messages but are "Repaired" messages.

Just updated a couple machines from 10.6.7 to 10.6.8 and it reminded me but I have been seeing it in previous versions of 10.6.