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Unless I'm a total moron.

GSdx 3068 MSVC 15.00 SSE4.1 0.1.16 plugin

but it no longer let's me set the resolution? I can only change the pixel size of the window but at 1920*1200 games are still in native resolution.

Yep, that happens from time to time. Just delete the ini file and configure it again.

To set the window resolution.
Config>>>emulation settings>>>window
or
Config>>>video(GS)>>>window setting

type in your favourite number in the custom window size boxes.

Internal resolution you can do it in gsdx.