Neil, the Ballistic is my old RIB...the staining on the seats first appeared when in my ownership and I assumed (rightly or wrongly) that it came from red dye on the lifejackets and red foul weather kit that were stored under seat pods -it always came off using starbright vinyl cleaner and I'd be surprised if that doesnt do the trick again. IMHO, it doesnt sound like a warranty issue, just part of the pleasure of having a RIB with a light colour scheme.
Not sure about the paint issues with the outboard either, but did you notice these when you bought her? As with buying a car, when you notice "defects" you negotiate the price accordingly - I thought that given the price you paid for her, these factors had been taken into account.
Incidentally, I've always found the after sales support from JBT to be first class and when they can help you, they will.