If you are experiencing motion that stutters, like its missing frames, and this is only occurring on iOS devices (iPad and iPhone) this is likely the case of the profile you have set it at.
Adobe Flash Media Live Encoder (FMLE) is usually set with an encoding profile of "Baseline" by default. This profile works best with mobile devices, in particular iOS.
Some installed devices might change this profile, though. To manage your video encoding profile, click the wrench icon next to the video format, which should be H.264 (not VP6).
After you click this, an Advanced Encoder Settings menu will pop up like below. You can use the drop down on the profile to change from "Main" to "Baseline", if it's not already set there. Changing this will remove the stuttering motion on iOS devices.