As with any measurement, a tight controlled protocol can greatly enhance the repeatability of the data. We highly recommenced that you pay close attention to the key points as outlined below.
For users that have noted that their jumps results are often flagged as High Variability. 
This is a good indicator to that the jumping protocol can be improved. 
Some variability is expected especially when athletes are new, but this then should reduce quite a bit once they are familiar with the task.. 
It needs to be communicated that each jump needs to be a all out best attempt..
Some key points to consider:
1) Ensure a good warm-up prior to jumping ( 5-10 mins) included some dynamic practice jumps
2) Mark the floor with a cross using tape - instruct athletes to stand and jump from the cross. 
With the counter movement,  reposition the stance each time between reps.
3) Place the GA PowerTool sensor on a small mass and position it vertically under the the bar or broomstick.( or better still follow point 4)
4) Consider permanently mounting the GA PowerTool above the athlete, if ceiling height is no more then 3 meters
this means you can connect to the velcro strap bar(or broomstick) directly in the center and therefore eliminate variation due to side ways tilting.
click here for more info
5) Ensure velcro strap is securely attached to the bar - you don't want it to be able to easily flop about and move around the bar because there is a large loop
6) Instruct the athlete to jump for height - give them feedback on height - but then observe variables such as mean mover or peak velocity. 
(Tip: if the athletes know what you looking for they often will try and cheat the system )
7) Watch the athlete closely and instruct them not to lift the bar from their shoulders. If their is unacceptable movement then repeat the set or delete the offending rep, by clicking on it in the list as its displayed on the iPad
8) Only press the start button once the athlete is in place - standing tall with the bar across their shoulders
  Press the Stop button immediately following the last rep - to prevent additional reps being measured
For addition information please read the measuring jumps tutorial