It would appear that the internals of GTK have changed the layout of part of the state associated with keycodes. Unfortunately thats an internal detail Geany doesn't control.
So my first suggestion is to try just editing the settings.conf file and replacing the old number with the new one.
Note: the numbers in hex are 0x4000044 and 0x6000044 respectively, ie the new number has one extra bit set, but what that means would have to be searched in the GTK APIs somewhere (in saying GTK I'm assuming Scintilla just passes keycodes and states directly from GTK)