We have mostly late 2012 Mac minis in all our classrooms (a couple 2014 Mac minis) and we are experiencing a strange issue wherein some Mac minis will boot to the Boot Runner 3.0 screen showing both Windows 10 and Mac OS X High Sierra or Mojave and other Mac minis will skip Boot Runner and just boot straight to Windows 10. On these “special” Mac minis even if I hold down the option key the only volume displayed is the Windows 10 volume. Holding down shift doesn’t work (just get a blank black lit screen) and Cmnd + R to recovery doesn’t see the High Sierra APFS recovery disk and instead tries to net boot and when it does net boot it boots to ancient Mavericks net boot image (late 2012 Mac minis).
So what is crazy is how some Mac minis work and others just don’t. I can swap SSDs all day long but the results are persistent.
The current startup disk is stored in NVRAM, so did you try zapping the PRAM and see if that resolves the issue?