Hi Aldevinas,
I thought you were using Mac, on windows the skype manage API Access Control setting is located in Options>>Advanced Settings>>"Manage Other programs' access to Skype", this is the place where you should see that Standard ERP is Allowed to use Skype.
And the Skype authorization (when you install SERP and launch the system) will be show directly in skype (in mac it is shown in a pop-up window).
I did a test just now with Skype 7.36.0.101 using a windows computer and it worked correctly when I tried to do an skype call using the Communication Centre. Do you receive a different message when press the Skype button?
To see more information about how skype handle 3rd party applications: https://support.skype.com/en/faq/FA12384/how-does-my-3rd-party-application-work-with-skype-and-how-will-changes-to-skype-impact-my-3rd-party-application
Regards,
Erik Muñoz
HansaWorld