Hey paolo,
we would need your Player.log to see if any issue occurred during loading.
Can you find and upload them?
Here is explained how http://brightrockgames.userecho.com/topics/118-how-to-submit-a-bug-ticket/

Could you create a savegame where this issue still occurs after loading?
This would make it extremely simple for us to debug that case.
Otherwise it is hard to reproduce and I don't recall running into such issue.
Cheers

I think the OP should be fine as units flee now always. In my opinion we should keep that unless anyone finds a problem with it.
If so, please report a new bug.

Just to give an update: It might happen that Unity 5.5 final gets out of beta during the next couple of weeks.
(https://unity3d.com/unity/roadmap)
This would fix the stutter problem for you guys.
With some luck it will make it into version 1.5 which is supposed to be released mid of December but it is yet unsure if the new Unity version will be ready at this time.
If not, it will be likely be in 1.5.1.
Stay tuned! :)

Did the last Patch resolve the issue for you? (it should)

See http://brightrockgames.userecho.com/topics/1275-placing-a-rally-banner-inside-the-arena-makes-it-unusable/#comment-7259

In version 1.5 Rally flags can not be placed into Prison nor Arena anymore as well the Shockwave spell wont hit units behind walls, obstacles or inside Prison/Arena.