I have a problem with perldesk that is causing it to send blank emails when users email in a new support complaint. I THINK it may be due to the template based system, but I am honestly not sure.

Anyone have a suggestion how I may troubleshoot this further?

Registered or unregistered users?

both

If you've checked the relevant templates, you may have to look into the code.

I assume the emails are being sent, and have the correct headers etc?

Had a similar problem - somehow one of the included files had been deleted / renamed.
This was newticket_registered.txt or similar.
Just uploaded the correctly named file and all worked again