Having to repeatedly stop a recording

[judge]

It is possible to stop any recording at any time, whilst recording call up your media file list, select the file that you want to stop (will have a red icon next to anything currently recording) then press the Red button, you will now be given a choice to Stop recording, Stop and delete, Stop after current event. (might be more or less options as doing this from memory at the moment)

The timer will kick back in on next autotimer poll though. I think that's the OP's issue?
So AT needs to be set up correctly or disabled when he has this issue.