I find that the Tools -> Options -> Keymap panel has duplicate entries for every one of my entries in the "File" category. If I assign a shortcut through the panel, that shortcut will immediately show for both entries.

Other categories (View, Windows, etc) don't have duplicates. 

Here is a sample registration:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE filesystem PUBLIC "-//NetBeans//DTD Filesystem 1.2//EN" "http://www.netbeans.org/dtds/filesystem-1_2.dtd">
<filesystem>
    <folder name="Actions">
        <folder name="File">
            <file name="com-mycompany-mypackage-MyAction.instance">
                <attr name="position" intvalue="201"/>
            </file>
        </folder>
    </folder>
    <folder name="Menu">
        <folder name="File">
            <attr name="position" intvalue="100"/>
            <file name="com-mycompany-mypackage-MyAction.shadow">
                <attr name="originalFile" stringvalue="Actions/File/com-mycompany-mypackage-MyAction.instance"/>
                <attr name="position" intvalue="201"/>
            </file>
        </folder>
    </folder>
</filesystem>

When I tried to do this with a virtually empty/new platform application, I don't encounter this issue. I do not know which other configuration item triggers this situation.

I also find that if I add this:

    <folder name="Keymaps">
        <folder name="NetBeans_hidden">
        </folder>
         <folder name="MyKeyMaps">
        </folder>
    </folder>

The "MyKeyMaps" profile will show, but none of the shortcuts I enter will work. They do otherwise.

Both issues prevent me from reusing the "Keymap" panel in my application.