Raspberry PI controlled LED strip flickering
I'll turn my comment then into an answer:

If your PWM is done in software it will flicker as the PI is not a real-time OS so regularly the CPU will have something else to do and your lights will flicker.

You can TRY to give our program a higher priority. The 'nice' command does that. Beware that a lower nice number is a higher priority. 

Better is to use the hardware PWM in the Pi. That comes out of specific GPIO pins.