Sorry that the logic level FETs did not fix the problem. Using non logic level FETs with logic citcuits is a frequent cause of problems.
Suggest next step is to narrow problem down to hardware vs software. Start a new sketch and put the absolute minimum lines in it to reproduce the problems. Just enough to set the outputs for one of the colour/brightness values that demonetrates the flickering problem. Cut out everything else, all the IR stuff and so on.