Some of the "IDE settings" seem to save but one of the most important ones won't.
I always un-check the "Allow placement of caret after end of line", that saved no problem. I then went on to set the "indent and braces" in "Code Style" before re-formatting, it just won't save, I've tried "apply", "OK", everything.
I'm on Linux (Mandrake 9.2), Java 1.4.2_02 and Aurora #977
Otherwise appart from the default fonts, which are awful, it seems to work fine.