bwong's workaround also worked for me. See this Github PR ->
https://github.com/puppetlabs/puppet/pull/5024
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https://bugs.launchpad.net/bugs/1593749
Title:
puppet apply with pip
I can confirm what Paul Hirst said above, it seems to happen when tool
tips or drop down menus. It happens with these types of windows: Menu,
PopupMenu, DropdownMenu, Dialog, ModalDialog, Tooltip, Notification,
Utility.
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Notifications steal focus from Widget Layer
