Hello, I have an atmega128 with freeRTOS and tried to create PWM signal on 2 channels. First I tried to use CLOCK/TIMER3, but there were some “delays” on it while task switching, the same is for timer 0 nad 2. I set modulation values in the task and thats all. Shouldnt it work independent? Do some interrupts form timer 1 created by FreeRTOS can afect it? Thank you in advance for your help.

If the PWM peripheral is free running then you should not see any delays. If it relies on regular fast interrupts then you will have to have some form of interrupt nesting for it to work reliably.