My account has 3 agents associated with it. When a user submits a feedback ticket, it creates it in Freshdesk and sends the same information to the agent's emails with the delimiter for us to send back to Freshdesk. Since the agent is submitting the email back to freshdesk, it reads the information inside the delimiter and populates the ticket fields with the information.

This worked perfectly fine as it always has until last Wednesday. All of a sudden, anytime the agent replies to the email, the delimiter vanishes in the ticket notes in freshdesk as if it reads the data like normal. Problem is, the values don't populate the ticket fields. Nothing happens, nothing changes, thus the ticket doesn't update and all the fields in the ticket remain blank.

After a lot of testing, I figured out that the problem is the signature & footer of our emails. When we click 'Reply' to the ticket in our Microsoft Outlook email accounts, our personal default signature and company footer automatically appear as it would for just about any company with a standard email setup. Then of course below that, appears the contents of the email/ticket that we are replying to (which contains our delimiter) just like every other email setup in existence. Normally, we just simply reply with the delimiter and it's fine. All of a sudden as of mid-last week, we apparently need to delete the entire contents of our company footer and signature every single time we reply to a ticket for it to go through. It's almost as if with our company signature/footer which has only basic text and no special characters (or any of our delimiter characters), freshdesk doesn't recognize us as agents anymore, even though it will still say "Agent Responded" on our dashboard.

Were there any Freshdesk updates perhaps in the last week or so that would cause this issue?

I checked https://support.freshdesk.com/support/discussions/topics/311685 for the January 2016 updates but saw nothing that could relate to this issue.