Lync 2013 has an interesting little quirk in that it likes to display a dialog following a successful installation, even when the install is performed using the silent install parameters provided by Microsoft.
This Lync install dialog requires the user to click "OK" after which the installation is officially over. Since PDQ runs installations in the background this dialog box is not displayed to the end user, and as such is never acknowledged. This results in a timeout (after the default 60 minutes) and PDQ Deploy is therefore not informed that the installation is actually completed successfully.
The actual dialog that the Lync install pops up is:
"Thank you for installing Microsoft Lync 2013. To begin, open Start and got to your Office programs."