Hi Martin,
couple of things to try but...before you do please make a copy of aircraft.cfg
1.Delete all in flaps section apart from flaps 0 section....Leave Flaps 0.
2.And/or change the following..if previous doesn't work(I had similar issues with SStSim and Flightsim's Concorde flaps sections)
[flaps.1] //Outboard Trailing Edge
type = 1 // 1 - tail, 2 - lead
span-outboard = 0.8 // 0.0 .. 1.0
extending-time = 15 // seconds
flaps-position.0 = 0 // degrees
flaps-position.1 = 0 // degrees
flaps-position.2 = 5 // degrees
flaps-position.3 = 10 // degrees
flaps-position.4 = 15 // degrees
flaps-position.5 = 25 // degrees
damaging-speed = 250 // KIAS
blowout-speed = 290 // KIAS
lift_scalar = 1.00
drag_scalar = 1.00
pitch_scalar= 1.00
system_type = 0 //Hydraulic
To this..
[flaps.1] //Outboard Trailing Edge
type = 1 // 1 - tail, 2 - lead
span-outboard = 0.8 // 0.0 .. 1.0
extending-time = 15 // seconds
flaps-position.0 = 0 // degrees
flaps-position.1 = 1 // degrees
flaps-position.2 = 5 // degrees
flaps-position.3 = 10 // degrees
flaps-position.4 = 15 // degrees
flaps-position.5 = 25 // degrees
damaging-speed = 250 // KIAS
blowout-speed = 290 // KIAS
lift_scalar = 1.00
drag_scalar = 1.00
pitch_scalar= 1.00
system_type = 0 //Hydraulic
Try this and let us know how you get on..
