You need to clear the interrupt cause of the timer component. Depending on the timer base (UDB or TCPWM) there are different APIs.
There is a Timer_ClearInterrupt() or a Timer_ReadStatus(), check datasheet of your component.
Willam Here is an example of the timer program it is running some where close to once a sec however I have not scoped it. It is also using a CY8C4247LQI-BLE-483 . It has a great example of the interrupt and clearing of it.
Many thanks guys, I added Timer_ClearInterrupt but still didn't work, but the example worked perfectly. Looked at my code a bit longer and threw it away and used the example. Excellent!