We are noticing that if we try to create a keyboard binding where one of the commands is from a plug-in (compiled scripts), the native Rhino commands take precedence, regardless of the order that they are in.
For example, I have a command called Dist3D that lists a distance in both imperial and metric after picking two points. If I try to bind that to a keyboard combination like Ctrl+E (or whatever) with a native command, like Line, Line will run first.
! _Dist3D _Line
The Line command will run first, then the plug-in command as seen here: