If you flash, it will overwrite any changes you made to /etc/bluetooth/main.conf so you will need to redo that change. If you do OTA then it uses apt-get which will preserve those changes. olighak and Jan, can you try to redit /etc/bluetooth/main.conf and see whether that works. you will need to stop bluethood and start bluetoothd as root after you edit /etc/bluetooth/main.conf but you should not have to do that after reboots.
Nokia-N900-42-11:/etc/bluetooth# grep -v '^#' main.conf [General] DisablePlugins = network,hal Name = Nokia N900 Class = 0x00020c DiscoverableTimeout = 0 PairableTimeout = 0 PageTimeout = 8192 DiscoverSchedulerInterval = 0 InitiallyPowered = false RememberPowered = true ReverseServiceDiscovery = true NameResolving = true Nokia-N900-42-11:/etc/bluetooth# stop bluetoothd bluetoothd (stop) running, process 4772 bluetoothd (stop) pre-stop, (main) process 4772 bluetoothd (stop) stopping, process 4772 bluetoothd (stop) killed, process 4772 bluetoothd (stop) post-stop bluetoothd (stop) waiting Nokia-N900-42-11:/etc/bluetooth# start bluetoothd bluetoothd (start) waiting bluetoothd (start) starting bluetoothd (start) pre-start, process 4786 bluetoothd (start) spawned, process 4787 bluetoothd (start) post-start, (main) process 4787 bluetoothd (start) running, process 4787 Nokia-N900-42-11:/etc/bluetooth# hildon-im-xkbtool --list ID 0, Name: "Virtual core pointer" ID 1, Name: "Virtual core keyboard" ID 2, Name: "TSC2005 touchscreen" ID 3, Name: "omap_twl4030keypad"