The CatTools timer is normally stopped when the CatTools Manager (UI) is opened.
Are you sure it is stopping on close of the UI rather then on open? You can test if the timer is still on by creating a simple activity (login test for example) and to schedule it to run every minute, start the timer, close the UI then watch the status of the CatTools_Client.exe process in the Windows Task Manager.
The CatTools_Client.exe is the program which communicate with your devices to capture data. If it appears busy on the turn of every minute, then the timer is on.