The gyroscope thinks it needs to orient the craft to the opposite direction that is locked on the nav sphere. When you activate the engines, they overpower the gyro and point the craft in the correct direction.
1) Load the DesignerCraft.xml
2) Launch up to about 1km in AGL
3) Turn off engines
4) Lock Prograde
Notice that the craft wants ot point in the wrong direction.
5) Enable Engines and notice that the craft then points in the correct direction.
This should be fixed in 0.3.4.0 however, crafts that were already created and launched with this issue will likely still have the issue. However, if you relaunch the craft, it should work correctly now.