Hi,
I'd recommend to change HCI_EXT_ClkDivOnHaltCmd( HCI_EXT_ENABLE_CLK_DIVIDE_ON_HALT ) to DISABLE right within stack, but if you did it after HCI init, it probably does not matter.
Can you elaborate more on the way your code works, please? Like, what timer ISR does and how it conveys event/message to higher-level task, and how that task creates waveform. I ask because I am not sure what to recommend without understanding the basic cause of delay.
Obviously, the interrupt itself has rather predictable execution time (if it is a critical section, of course), but once you return control to OSAL, there is no way to predict delays e.g. between events. You may want ro consider creating your own task with high priority, and move it up the task queue until radio part of stack fails. Not best design practice, I admit.
BR,
Oleg