Hi thisisme,
I just thought I'd post my water damaged and stained eaves to show you.
This one was taken on 4th July 2009. The roof scaff had gone, but they hadn't replaced all the tiles, so when it rained, it rained straight on the inside of my eaves....leaving this:
...and this is the stain as of today, which has slowly become darker as time progresses:
It's being repainted with a stain blocking paint as part of my 12 month maintenance, thankfully! Now assuming the painter did the 'correct' thing, I'm guessing the eaves sheeting would have had some sort of exterior primer painted onto them before the top coat (white). Unless a stain blocking primer is used, then this will continue to leach through the paint.
Just keep a close eye on the underside of the eaves, especially now they are up and rain is forecast again. I hope your roof is finished too! Mine 'looked' finished for ages, but the roof scaff was still up...which meant tiles off in places and wet eaves!
Fingers crossed for you!