What Blender version are you using? Blender 2.75a has got the FBX exporting scale correct as far as I can tell. But something to try would be to got to your scenes tab in blender and change your Units to METRIC. Then right after that create a basic model(cube) and check your transform Dimensions(hotkey is “N” this should now be in meters and not units) note mine is 2m X 2m X 2m
Use the FBX exporter and if you are using BLENDER 2.75a don’t change anything. If you are using 2.74 or below you would have to set your scale to 100 also select mesh only and highlight selected objects(of course it only exports selected object then) See below all the screenshots.
