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Sometimes, there's stripes all over the screen on certain levels. It doesn't happen only on native resolution, no matter of graphic plugin settings.
It's not because of interlacing, it happens on "no deinterlacing" too.

My setup is
4713 svn
DX11 hardware 1980x1080 stretched to fit

Screenshot
http://img-eburg.fotki.yandex.ru/get/470...caf72_orig

Can you post a screenshot of other levels where that happens?

Is it only the underwater levels?
If so it's expected as it works fine in native res.

Yes, it only happened in underwater level so far, but there it disappeared halfway through the level.

In native res it's fine everywhere.

Well then as I said it's expected, there are glitches that only happen in higher resolution than native since the games are designed for that one (native) resolution.

You can try using the "Skipdraw" hack, check the "GSdx > Hacks" subsection in the configuration guide to learn about the hacks and how to sue them:
http://forums.pcsx2.net/Thread-Official-...v0-9-7#Gfx