I think it is quite certain this has absolutely nothing to do with xine. I get this with mplayer as well as vlc. This is probably a bug in nVidia's Xv support (the blue box is the index colour for the overlay, that the card is supposed to put the video in, but for some reason it does not).
Anyway, wish I had a solution for you, but just giving a bit of insight. I'd also like a solution, as it's very annoying.
One thing you can try, is using a different Xv port. On my system, I have three. Run xvinfo and search for the "port base" stuff. On mplayer, you can do something like "-vo xv
ort=123". This does not actually fix the problem, but it does let you at least postpone killing X until all the Xv ports are fsckd. (should be noted though, that I can't do any brightness/contrast setting in mplayer if I specify another port).
Anyway, hope you find your answer. The same problem is annoying the hell out of me.