but I wanted to use timer controlled interrupt handling to keep the effects stable and clean
...This is also why interrupts are allowed on the due, but not on AVR w/WS2812's, because it turns out that it is really really really difficult to write a useful AVR interrupt handler that will run in under 80 cycles...
Quotebut I wanted to use timer controlled interrupt handling to keep the effects stable and cleanCould you elaborate on that? What are you going to do?
Have you declaired the variables used both inside and outside your ISR as volitile?If you have and still have the problem then post your code in code tags.
Daniel Garcia wrote about it on G+ today: