For winds to be accurate, you need:
Accurate magnetic heading
Accurate OAT
Accurate Altimeter
Accurate Airspeed
Accurate GPS info
Any of these could cause the wind to look weird if it were off.
Are your winds stable when you are on a stable heading? If they don't move when you are straight and level, but are different from before when you turn, then it's probably an iffy magnetic calibration. If they are changing while you are turning, well, that's kind of expected because the GPS data lags the real world by up to a second. We try and filter as much of this out as possible, but maybe we can do better.
It's also possible that the Skymap outputs data slower or different than we expect and that's causing problems. Some more detail on exactly what it is doing and when would be helpful.