Rogaine use causing flaking of scalp?

No, the irritation on your scalp doesn't correlate with whether or not the Minoxidil will be effective helping your hair to grow. There are options you can try to alleviate these effects, including some shampoos or other products. If you're unable to find someone to ease the side effects on your own I recommend speaking with your doctor.

The flaking with minoxidil can come from a few reasons, including irriation and worsening of seborrheic dermatitis. It does not correlate with lessened effect. More frequent shampooing, use of anti-dandruff shampoos and sometimes addition of a corticosteroid are all options I use for my own patients to combat flaking (depending on the cause).