Email command not working from script automated email.

One way we use our helpdesk system is to keep track of computers we loan out to students. We have a google form set up where students put in their name, homeroom, what computer they need and why, etc. When they hit submit, google script adds their info to a google sheet as well as emailing all the info to our helpdesk email. I've set up email commands to parse the emails as they come in, but this is where the problem lies. The email that google script sends is NEVER parsed... Now... I can take this EXACT email that google script sent, and send it from my personal email account, same subject, same body, literally everything the same... and when I email that to our helpdesk, it is parsed properly... so I know email commands are set up properly, it just has to be something with how google script formats the email or something along those lines, because ServiceDesk never parses those emails, and I really need to be able to configure the REQUESTER... Anybody ever run into this issue? Any ideas?