I have TIMER2 running at 500us interval. ANT is working as 100Hz master. Understood softdevice will affect the timing and cause some latency. I am guessing it is delaying the TIMER2_IRQHandler response by more than 500us which is enough to miss a TIMER2 interrupt.
I am using TIMER2 as a local communication logic to talk to a device and debugging some issues. Looks like the softdevice is occupying CPU too long. I hope it is not, otherwise I will have to add extra hardware to do the communication :-( which is BAD. :-D