Seems like I found a bug in ILT (Item Level Targeting).
When you copy items in GPPs that have "Apply once and do not reapply" selected,
the Filter-ID won't be changed.
So the new item has just the same ID.
For example if you use the CSE "Group Policy Files" and copy items,
only the first item will be processed.
If you have let's say three items (that are copied), there IDs would all look like this:
<Filters><FilterRunOnce hidden="1" not="0" bool="AND" id="{2B28F5C1-237A-4EDB-8318-F2B862493D89}"
If the item is processed, CSE will create the key for the ID in HKEY_CURRENT_USER\Software\Microsoft\Group Policy\Client\RunOnce
"{2B28F5C1-237A-4EDB-8318-F2B862493D89}".
The next two files will fail, because the RunOnce key already exists.
MVP Group Policy - Mythen, Insiderinfos und Troubleshooting zum Thema GPOs: Let's go, use GPO!