OK, looks like it is fixed.
I had set DCS to Run in Administrator mode, and TrackIR was not set like that. After I changed TrackIR Properties to Run in Admin mode the TrackIR button assignments work correctly.
Here is a mission file from @Black6 that I am going to work with. One of his scripts does the 'detect enemy aircraft with search radar'. I am hoping to use this for low level flight Blue ac vs a Red SAM site. I am starting with this from his mission..
Do Script
-- Flat Face detection
local DetectingUnit = Unit.getByName('P19')
local TargetUnit = Unit.getByName('Tiger-1')
if Controller.isTargetDetected(DetectingUnit , TargetUnit , Radar) == true then
trigger.action.outText('detected by Flat Face', 10)
trigger.action.setUserFlag( "11", true )
end
Wrecking Crew's post in DCS - Mouse Won't Pause TrackIR Anymore was marked as the answer