with chameleon 2169 and up chameleon now has persistence with the boot flags you enter at the chameleon prompt it will store them even if you shut down or reboot. make sure you clear your flags. and like herve said if you have multi partitions chameleon will only respond to the org.chameleon.Boot.plist on the partition you originaly installed chameleon too usually the first partition with osx after the small efi one. in my case i have to edit my lion Boot.plist to affect my ML since i had lion installed first.