@Kayan – I see the same problems with keyboard shortcuts sets. After a restart of InDesign the assigned KBSC of a menu generated by a startup script is removed.
I found no solution to that. Just a hint how we can edit the indk file, but this will not help at all:
Make a new KBSC set. Assign a keyboard shortcut to your startup script.
Go to preferences and open the new indk file in a text editor. Find the menu name for your menu action and look at the code:
(I did this with a startup script by Gerald Singelmann)
Assign a keyboard shortcut in the UI.
The code for the KBSC is defined in XML notation like that:
<shortcut><action-id value="0xff002000 + 1" name="KBSCE Scripts menu:.Group Remembers Layers"></action-id><context>DefaultContext</context><string>Ctrl+Cmd+G</string></shortcut>
As long as the session persists this is working.
But the next time InDesign will be restarted the the value of action-id will be changed and the KBSC cannot be found in the GUI.
Uwe