Are your external USB HDDs plugged in when the 'boot order changes'?
Plug in all your external drives, enter BIOS and then set the boot order priority as you want. Save and then exit.
If an external HDD is set as default boot device, when it is disconnected, BIOS won't try to boot from it first, but if you restart your PC (eg when Windows updates itself) with this drive connected, then your boot order may 'appear' to change, as BIOS now finds this drive and attempts to boot from it.
That is the only explanation I can think of. Windows cannot alter any BIOS settings to change boot priority.