Just to confirm that the Just Flight addon isn’t causing the issue, try uninstalling it and see if anything changes.
One thing to bear in mind, do not arm the spoilers in a Boeing before takeoff, unlike an Airbus.
Boeing spoilers will deploy if they are armed, and weight is on the landing gear.
The ILS radio in the Boeing 787 requires both a frequency and runway heading to be entered, it will not take just the frequency.
In Controls Options, when you click on “Search by Input”, and move your throttle, what command is displayed?
If you haven’t seen this, it may offer some help with the 787: