Flaky paint itself isn't a problem, oxidised paint or frames is (UPVC can oxidise too).
For me the solution is to wash and scrub frames very thoroughly the first time, do a few windows then go back and re-do the glass only.
Once you gain some experience you can usually cope ok with this work...
On frames where the woodwork has been exposed for a long time, the wood absorbs some of the water and then releases it after you've gone leaving spots and marks, tell em' tough luck on upstairs and squeegee off ground floor (I still use WFP on them, but tidy up with squeegee)
I won't get out ladders to clean upstairs windows for anyone, only use them for access to flat roofs and so on.
I'll only compromise on ground floor work, and not at all on georgian or leaded!!
Ian