Setting EXE files in AVG won't do you any good, it's most likely timing out or blocking the services running on the server as well.
Are you actually using the server protection version of AVG?
If you have a dedicated filemaker server, is antivirus even necessary? The industry trend says that it's questionable to have antivirus at all on a dedicated database server. (IE this help article: http://dba.stackexchange.com/questions/19903/is-it-safe-to-run-antivirus-software-on-my-database-servers )
I would focus my work on the network hardware and software firewall security, and drop AVG.
Thanks for your response (and associated links). I am currently just running it on my desktop since its just the free copy of the server and am using it to learn.
When I get to the point of setting up the server I will not install AVG, thanks for teaching me that. I was not aware that antivirus should not be installed.
For the moment AVG has an option to disable it for X amount of time. So I am using that whenever I need to work with the console.