Overlap problem

So recently i have been working on a kinda “moving” object that simply goes for right to the middle and then to the left

BOX–>1secBOX–>1secBOX
-----------Platform---------------

and all this reverted blablabla

Now my problem is my fps controller needs to jump on the Platform without that the box “hits him”.

So when i jump on the platform and i am too late the box overlaps with the fps controller. Now all my collider scripts wont function when its overlapped. So what can i do so my collide scripts work even when overlapped.

Javascript recomendet.

Any help will be appriciated

Could it be the problem described here:
http://www.codingjargames.com/blog/
Check for “Bad Physics Code”