IIRC this popup is that the n900 is recognizing it with the wrong plugin used to something else. You have to go to
/etc/bluetooth
and edit the file
main.conf
and make your DisablePlugins line look like this:
DisablePlugins = network,hal,input

then restart and try again.

PS: You will have "problems" with the keymapping if you try to connect a bluetyooth headphone first and the dualshock latter, always do the dualshock first.

There's the possibility of custom keymapping by editting
/usr/share/hal/fdi/policy/20thirdpart/20-x11-sony-sixaxis.fdi

PSS: Do all of it as root.