I do not have any knowledge of your particular equipment, but it does sound like you need the average speed "dampening" for want of a better description.
On some units for commercial use you can set the time period for averaging speed, such as over 10 seconds, 30 seconds 1 minute etc. The longer the period the more stable the speed, but if you change speed quickly, it will take a few seconds to display the correct speeds.
On our units on my vessel the speeds are very accurate down to 0.1 or 0.2 knot, and that is in areas where we do not have differential GPS coverage.
Try looking in the manual to see if you can set this averaging, or dampening period, and try increasing the period slightly to iron out the highs and lows. If you dont have that facility, sorry I cannot help!