A number of changes in the user interface over the years have caused problems for users, and Linden Labs keeps tweaking the user interface to try and solve supposed problems. I suggest instead of further tweaking, implement a general command-action mapping function and see what users select.
Suggested user interface would be a dialog box with one row per action:
Start Run =
Control ( ) Shift ( ) Alt ( ) Hold ( ) Double [Key... |v] [R]
Stop Run =
Control ( ) Shift ( ) Alt ( ) Hold ( ) Double [Key... |v] [R]
This change would be implemented by the user by changing this to:
Start Run = ( ) Control ( ) Shift ( ) Alt ( ) Hold
Double [Key...|v] [Forward]
Stop Run = ( ) Control ( ) Shift ( ) Alt ( ) Hold ( ) Double [Release Key|v] [ ]
If a user selects "None" then no key would be bound to that action.
A single menu item for "Restore default keys" and "Restore 'None' Keys" would provide a safety valve.