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Thanks to Ivalics assistance we're able to resolve this issue.
The issue was due to changes being made to the /conf directory for the domain when installing an Application via the Application Vault (specifically Joomla pkg from http://www.apsstandard.org/). When installing this package it creates a sub-folder in the users conf directory called /siteapp.d which contains conf files for specified packages altering the php handlers for the specific folder and breaking suphp, hashing out this conf file corrects suphp.
As a global solution we've altered the affected packages on the server so that they:
-Don't create the conf file
-Don't change permissions to 777 for folders/files so applications will work under suphp
We did this by editing the APP-META.xml located in the pkg directory: /opt/psa/var/cgitory/<packagename>
As per this Parallels forum thread (http://forum.parallels.com/showthread.php?t=97843), excluding the permissions/handler sections in the <mapping> area allows the pkg's to install correctly for suphp requirements.