While the sync option is on, Start11 imports whatever the Windows menu has pinned each time you sign in. Removing a tile inside Start11 does not unpin it on the Windows side, so anything still pinned there arrives again on the next boot.
Order matters when you try that setting. Turn the sync off, sign out and back in, and clear the three tiles after that. On the Windows 11 and Windows App styles the same option carries a "(sign out required)" note, so give it a sign in cycle to take effect before you remove anything, rather than removing them first.
If you would rather leave the sync on, unpin Settings, File Explorer and Edge in the Windows menu itself and there is nothing left for Start11 to bring in. Ctrl and a click on the start button opens the Windows menu, as does the right Windows key, if those options are enabled on the Control tab.
One thing about the reinstall you already did: it was never going to change this. Your Start11 settings and the Windows 10 style pin list live in your user registry, and a normal uninstall leaves them in place, which is why there is a separate purge file for a genuine clean slate. No need to reinstall again for this one.
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