I've ran into this too, and am glad to see that a simple restart fixes it; I'd be glad to help, but am a ToME newb, to say nothing of ToME dev & debugging; if there are any logs or information that may help, just let me know. The issue persists with all add-ons disabled.
I did take a log at my games log, but there doesn't seem to be anything informative there;
the second rebind is manually setting it back.
Code:
Binding #{italic}##AQUAMARINE#Secondary Hotkey 2#{normal}# to sym:_g:false:false:false:false :: 1
[LOG] Rrene uses #{bold}##ORCHID#Stunning Blow.#{normal}##LAST#
Binding #{italic}##AQUAMARINE#Secondary Hotkey 2#{normal}# to sym:_2:true:false:false:false :: 1