Ford Focus transmission failure warning

I have a 1.6 Zetec Focus which I did not use over the winter. When I tried to start it after a few months, the battery was completely dead. I tried to jump start it and I started getting the warning message "transmission failure" and an alarm sounds and it wouldn't turn over. I tried to jump start it and this didn't work. I replaced the battery with a new one, but I keep getting the warning message and it does not let me turn the engine over. It is a manual gearbox, so I am confused how it could fail. I thought that as the battery was completely drained, I might need to "reset" something in the car?? It was fine with no issues previous to this.
Can anyone give me any advice??