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DEM's processing of default apps consists of two parts: collecting the settings from the profile archive, and applying those settings. The first part happens during the path-based import. For the second part, we need to wait until File Explorer has started, or it might/will trample all over the settings we just applied.
To launch that second part, we add "C:\Program Files\Immidio\Flex Profiles\FlexEngine.exe" ::DefaultApplications to Explorer's RunOnce key, so that we automatically get to run when Explorer is up. Looks like that's too late in your case, and that the startup folder gets processed before that...
As a test, could you try adding a shortcut to your startup folder (with a name "alphabetically before" the name of your problematic shortcut) that runs ...\FlexEngine.exe ::DefaultApplications? Or maybe turn your current shortcut into a script that runs ...\FlexEngine.exe ::DefaultApplications, and subsequently launches the "real" item, just to prevent any further timing issues?