Hm, first things to check are your different range settings, e.g. battle range, AI range, etc. (in Battles > Battle Settings, as well as the individual battle system's move AI range).
Next would be the use ranges for the abilities and items - in real time battles they're usually limited, so make sure that's correct.
Also, since you're using real time battle areas, make sure your default battle system (or the combatant spawner overrides) is the same battle system as your real time battle area's system. Otherwise, e.g. if that's turn based, the combatants will not take part in real time battles.