/PAE is needed to be able to use AWE. However, not always. Books Online says:
In Windows Server 2003, PAE is automatically enabled only if the server is using hot-add memory devices. In this case, you do not have to use the /pae parameter on a system that is configured to use hot-add memory devices. In all other cases, you must use the /pae parameter in the Boot.ini file to take advantage of memory over 4 GB.
But maybe your server is configured for that. Because all other output indicates that everything is OK. Just for a check, can you post the the first five minutes of the current ERRORLOG for this instance?
This CLR dll you are having problem, from where did you get it? Is it something you can share? Also source code?
[font="Times New Roman"]Erland Sommarskog, SQL Server MVP, www.sommarskog.se[/font]