@pterobyte - Thank you for pointing me in the right direction. I have finally solved my problems after checking out the logs that you suggested.
After looking at the amavis log, I saw the following -
"(!!)TROUBLE in pre_loop_hook: db_init: BDB no dbS: __fop_file_setup: Retry limit (100) exceeded, File exists. at (eval 85) line 324."
The line above it was trying to create a db file -
"Creating db in /Library/Server/Mail/Data/scanner/amavis/db/; BerkeleyDB 0.49, libdb 4.7"
After googling the information that I now had, I found out to delete the .db files in /Library/Server/Mail/Data/scanner/amavis/db/.
Here are the steps that I took to fix after the information that I had:
1. stopped mail server by running sudo serveradmin stop mail
2. deleted (or moved them, in my case) all .db files from /Library/Server/Mail/Data/scanner/amavis/db/
3. enabled AV, spam and junk filters in the server app
4. started mail server by running sudo serveradmin start mail
5. Once the mail service started back up I reloaded postfix by running postfix reload
*Note that anybody doing this, you will need root access to perform some of these tasks.