Ordinary click just stops working. Only simulated click works!

So, we have processes that are running 0-24 for some time now. As of yesterday some of them just stopped working when needed to click on an element. If we set it to simulate click it works. How can that be? Some of the processes on the same machine works fine.
We noticed that on the process where it does not work the Internet explorer browser is orange at the taskbar, like it is not activated.
We tried to activate it but it wont help EXCEPT we manually click on the browser and then it works.

Anyone had similar problem ?

This seems to solved our problem:

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