As far as I know you ned to keep track of what HW timers and counters you use your self :-) One thig to keep in mind is that if you use the HPWM in your pic that also steals a timer, usually timer 2.

I hope you use DT's instant interupts since that is the only way in PBP to get the interupts to be performed when the happen and not as in PBP's usual way after the current command is executed.

I would set up a timer to overflow every 0,1 sec as a RTC timebase and use that one to get the 3.6 sec (by increasing a variable in the interupt routine). By doing this you can have many events with different times beeing executed.