I got serious flaking a few times when I first started minoxidil... but quickly realized a correlation between the few times I had flaking and the few times I got a little overambtious in my early days and applied more than 1ml of minoxidil! Using more than the standard dose caused flaking for me, especially if I did two doses with no shower in between. (Hey, no I am NOT unsanitary, I just like to wake up on Sunday sometimes and watch football until noon without showering... that means my am minoxidil went on without a shower, and I flaked that night.)
Nizoral helped me, but it does not help everyone. My flaking actually stopped, but once in a blue moon I still do notice a stray chunk of dead scalp stuck in my hair when combing my hair in the mornings. I just flick it away, and that's it. It comes with the territory.