Actions in performed in the Path of Exile client are input emulated by EB. This means the mouse is moved and the buttons are pressed. For melee skills, when you don't use attack in place, the behavior you are describing comes from the inaccurate targeting of monsters due to the way they have different hitboxes. Quite literally, the attacks are resulting in movement actions behind the target (which can be exaggerated if the target is moving towards you).
Using AoE based skills and attack in place is the most helpful, but you do have to be wary of desync still, and the OldRoutine implementation doesn't handle it at all. In 3.0, a lot of the skill targeting issues in the client that EB triggers are being addressed (as in the game client itself has fixes), so coupled with a better CR in the future, there should be less of this for the part, but the core issue of EB not knowing how the client will target a monster cannot be solved.
Basically, single-target non-aoe melee skills are just not that good in Path of Exile, so that's why EB struggles with them. The game heavily favors AoE based attacks, so I would suggest going for those types of builds, even though OldRoutine is to blame for some of the problems.
