These two applications are looking under /run for reboot-required and reboot-required.pkgs. The reboot-required file is just a string indicating a reboot is needed, the reboot-required.pkgs file shows which package(s) are calling for the reboot. If you really want to know why your getting those mssgs, take a look inside the latter file.
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[Solved] - Cairo Dock suggests frequent reboot after many package updates
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