Right so I had the time to test out both PWM and the most recent schematic and here is what happened:
With the capacitor, I still had weird behaviour whereby the LEDs where doing a slow stop rather than a slow start.
When I tested PWM I was very happy and satisfied as I could control them super smoothly and I am going to settle on that solution.
Thanks crutschow for your simulation and everyone who contributed. Much appreciated. For anyone coming after here is the final circuit which worked.
I have 13v across R3 when the LEDs are OFF and 0v when they are ON
I have 0.758v across from the collector to the emitter when the LEDs are OFF