I find that if I have taken over a new job that hasn't been cleaned in a while or had a naff window cleaner before, it can take a few cleans to get the sills right. But once they get a good regular wfp'ing they will pretty much stay clean.
It's also expectations from the customer too. Are they expecting every single teensy piece of dirt to be removed or are they being realistic (same with the windows), no matter how good you are a funny customer can find a problem somewhere.
Perhaps ask her nicely if she can show you a sill from the inside upstairs that is bad so you can learn and improve. Worth a try and it may help you see where you are wrong...or see if the customer is pointing at microscopic dirt and complaining!