OK. This one drove me nuts for quite some time before I finally figured it out. I hope this is of help to anyone who ran into the same issue.
With FileVault on, Bluetooth always came on and appeared in the menubar upon reboot no matter what was done to shut it off and remove it from the menubar.
I shut off Bluetooth, pulled it off the menubar, locked the prefs for it, locked the prefs for systemuiserver, and restarted. Lo and behold, bluetooth is on and in the menubar every single time
After yanking prefs and clearing caches, I was about to do a complete reinstall of everything when I remembered I had FileVault on. I shut it off, rebooted, and things behaved again.
Something about Filevault is definitely off. Maybe the prefs are not completely decrypted when the system tries to read them - there is a failure, then default prefs are used. Until this is addressed, I have shut off FileVault. There is a slight fear of things going horribly wrong and having all of my stuff permanently encrypted.
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