The initial setup which caused this issue was an Inventory Panel connected to the controller via item conduit (with needed awareness Upgrade). I used 4x4 Drawers.
The Controller does not accept items once it filled one slot of that given item.
As an example: I filled my setup with cobblestone, It accepted it nicely until it hit the 512 threshhold (8stack max of 4x4 drawer). After that it would not search for the next free drawer space.
To test this I then placed one cobblestone in a free drawer. It instantly accepted Items again.

I reproduced this issue with a new setup, filling the controller with buildcraft pipes.
I also reproduced it in another world with all the other drawer types.

Conclusion: The search for a new space, once the last one is full either is never called or broken.

I use the Mod in FTB Infinity 2.6.0 (I play on expert mode)

The system accepts items flawless, if they are inserted via a logistic pipes network.
So the issue probably lies with ender io. Therefore I am closing this.