By default Skype is not blocked as many other signatures so please check if IPS is blocking it.
You can disable it for example if you go to policy set on resources and customize this signature for in and out to be disabled.
Or you can check change the setting for this signature to be not block and put some auto ACK for exaple.
You can remove the signature from your rulset.
You can do some attack filter like any any and latter assign it on this signature for in out.