roberth I wouldn't expect osTicket Awesome to cause this issue, although I've just tested it on my clone system and %{ticket.thread.lastmessage} (without the .body part) includes the entirety of the user's last response, including the email header that was above the "-- reply above this line --" part.
If you're able to set up a clone too, it might be worth setting one up and restoring all of the stock files. If the issue is sorted there, you know the problem is due to osTicket Awesome and can report it on their forum (it's then up to you whether you revert to stock, or stick with the issue until it's fixed). If the problem still occurs with stock files, then there's an issue elsewhere.
Edit: note that I don't use osTicket Awesome - all of my testing is on the stock version