The former is just fine. Either add Fn to that, or switch the preference in the keyboard preferences.
Pressing fn-ctrl-F2 does not bring up TM's context menu on my Macbook Pro.
I think you meant fn-option-F2 ... but you should try option-fn-F2 (seriously :-) .. the order which you press the keys in the combo seems to matter when using fn to toggle the FKeys
-steve