Hello Stephen,
The issue may be that when you invoke Exchange cmdlets from the console, you perform the actions directly, but when you invoke some Exchange features from Adaxes PowerShell scripts, it is a remote call anyway.
Can you send us some of your scripts to support[at]adaxes.com? We need to have a look at them, then we may have some suggestions as to performance improvements.
Do you plan to implement Lync management too ?
This is in our TODO list, but not for the nearest release.