If for any reason you cannot run our diagnostic script please follow all the steps from http://www.codetwo.com/kb/diagnosing-codetwo-exchange-rules/ except for step no. 5 and additionally proceed with the below ones:

1. Export set of rules you are using in your CodeTwo Exchange Rules.
-Exchange Rules PRO > http://www.codetwo.com/kb/212
-Exchange Rules with the new interface i.e. 2007 3.x & 2010 2.x > http://www.codetwo.com/kb/248
-Exchange Rules with the old interface i.e. 2003 http://www.codetwo.com/kb/32 and 2007 2.x or 2010 1.x http://www.codetwo.com/kb/33 (linked KB articles cover different issue but explain where templates and rules are stored as well)
2. Export detailed log files, see a manual from point no.1 for details about log files location.
3. Tell us what is your MS Windows version?
4. Tell us what is your MS Exchange Server version?
5. Execute this PowerShell cmdlet in your ems Exchange Management Shell and copy or take a screenshot of the result: Get-TransportAgent
6. Execute this PowerShell cmdlet in your ems Exchange Management Shell and copy or take a screenshot of the result: Get-RemoteDomain | fl