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You can try setting the zoom to about 103%, could fix it

EDIT: From http://wiki.pcsx2.net/index.php/Shadow_of_the_Colossus
Flickering Borders
Type: Note (not an issue)
Description: Enabling the "Half-Pixel Offset" hack to realign the textures results in flickering white lines along the top and left borders of the screen.
Workaround: Adjust the Zoom in the main emulation settings to 102.60%, and set the screen display to "Fit to Screen/Window". This will cause the game to take up the full computer screen with just enough zoom to bypass the flickering borders. You can then adjust the display in-game in the options menu to your liking (4:3 or 16:9).

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Yeah but that shouldn't be necessary for this game. Can you take a screenshot of the problem? (Or even better, possibly a video of it if you can, since you mentioned it's vibrating?)

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Yeah I see what you mean. Though I don't have it as bad as you do. In my case it seems to be like a one pixel border that appears from time to time. In Luke's Manor for example it's clearly visible (but still only 1-2px, but in Sheridan it was almost completely invisible.

[attachment=54934]


[Edit]

In this battle it's hard to notice again. It seems to blend in a bit.

[attachment=54935]

It's definitely caused by the fix for ghosting though. Most likely because it moves the stuff around a bit, and that might cause that glitch to occur.
I don't think much can be done about it without breaking ghosting again. :/

The thing with 102% works if you have 16:9 monitors, but if you set it to "Stretch to screen" on a 16:10 monitor like I do (1920x1200), it'll stretch out everything in a wrong way instead of sticking to a 16:9 format. And setting it to forced 16:9 kind of crops things off, or makes it blurry in areas.

If it is a one pixel border it might not scale with upscaling. Therefore this border will be less visible with 4xnative than native...

Hmm just tested that theory, but it's the same on all scales. But for native it actually doesn't show at all.

actually one can check the new development builds including gregory's hacks. They might solve the misalignment without introducing new errors. It specially fixes upscaling issues.

You mean apply the ghosting patch and combine it in use with gregory's hack? Or try it without the patch first? I'll go download 1.3.1-182 for starters from buildbot. (I'm still using 1.3.1-20 lol)

[Edit]
The Align hack doesn't fix the ghosting. So it'll still need the patch. But I can at least compile a GSdx version of this recent one and see if the combination of the two fixes that border.

[Edit 2]
Tried combining both gregory's hack and the ghosting patch, but sadly it doesn't fix the border effect.