The rubber seal have oxidized Darryl, I found the only way to cope with them was to wash with applicator very carefully, try not to 'wash' any of the seals themselves, stay just shy of all the edges, squeegee neatly and don't do any detailing, and whatever you do DON'T TOUCH THE RUBBER SEALS WITH YOU SCRIM!!!
Use your squeegee to blade off any access water on the frames.
I'm sure you would have found that it is using the scrim (or microfibre) that made it a nightmare, and that even the lightest touch between scrim-seal-window frame left a horrible black mark that was next to impossible to get rid of
These are usually windows that catch the full sunlight, often those on the other side of the house are not to bad.
Explain to the customer that the sunlight has caused the rubber seals to perish and oxidize and appologise profusely and tell them that you dare not detail the edges with your cloth as it will make the most awful marks on the frame that cannot be removed (Yes yes, I know, with things like T cut and so on you can get them off, but its easier if the customer thinks it is next to imposible to do so)
So they may see the odd little mark on the edges of the window.
I now use WFP, so this isn't a problem now, doesn't seem to happen with WFP, but that might depend on how badly perished the rubber seals are, I've only come across a couple with my WFP, and they had not gone to badly.
And don't get your applicator to wet either!!
Ian