You mean you're getting a message saying "Airspeed above flap extend speed" or something like that?  Go into the aircraft.cfg file and look for the [flaps.0] section.  If your aircraft has more than one [flaps.*] section, you will have to do this to all of them.

Wherever you find an entry labled flaps-position.*, you will find two numbers following it.  The first is the angle of the flaps in that position.  The second number is at what speed the flaps may be deployed to that position.  Just set the speed higher to get the flaps down at a higher speed.

That's basically what I meant.  Just follow the instructions given above and that should fix the problem.