I had flaking from minoxidil as well... I pinned down the cause. After thinking about my routine, I realized that the flaking occurred after doing two activities...
One, was applying three doses of minoxidil without a shower in between any of them. Yep, that's right... woke up on a Saturday morning, showered, and applied minoxidil. Then went through my day and got home. I had no evening plans, just waiting for my female companionship for the evening to arrive from her family gathering and she wasn't due back for 3 hours, and thought we would probably shower together, so I thought it a good opportunity to apply another dose before her arrival. I did. She showed up and we shared two bottles of wine, had sex, and then went to bed with no shower. The next morning, she cooked us breakfast and left. Since I was really tired, and it was football Sunday here in the US, I said f*** the shower I'm feeling too lazy lets stir up a bloody mary or two and take in the early game in my bathrobe. I got up to pee, looked at my tired unshaven mug in the mirror, and thought it was another great opportunity to do my minoxidil, and did another application. After the end of the early game, and a nice nap, and lunch, I thought it time to hit the shower. I did so, and when I got out and combed my hair I noticed flaking. I had a second occurrence of this (3 minoxidil applications w/o shower) and the same thing happened. If I shower between at least two of the minoxidil applications, I have no flaking issues.
The third time this happened to me was one late Saturday night when I got home from some evening activities, looked in the mirror, and said f*** this I'm going to f*****g kick-start this sh*t and give my hairs a right royal dousing of Minoxidil. I did so, and it was a 2.5ml orgy of Minoxidil madness! When I woke up the next morning, I was flaking. Showered, and shampooed with Nizoral and it pretty much was gone after that one treatment with the nizoral, on all three occasions.