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There are two logger's settings nodes in Tools, Options... in Orion build 011003_1.
I updated my build and tried this out. I don't see 2 logger settings nodes. Do you still see this in the 11/05 build? (My code was updated at 5 Oct 2001 16:24:38 GMT) Mayb this problem could be related to the fix for bug 15947, which was fixed on 3-oct? http://openide.netbeans.org/issues/show_bug.cgi?id=15947
You are right, now it works for me too in build #011007.