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Alright i attached the bmp as asked an here's the problem, the reflections off of lakes and other bodies of water in Mgs3 Subsistence and there is also a noticeable drop in framerate when the reflection glitch appears on screen. However, it disappears when I set it to software rendering.

I was wondering if there is any known reason for this, because I tried it on other computers and the same glitch occurs coupled with a framerate drop.

Thanks

ps if you want the gs file ask but its too large to have as an attachment

The game is severely bugged in the hardware plugins, only way to get everything looking right is probably the software renderer in GSdx. There has been many other effects removed cause they looked just like that glitch and that one is just one of a few still remaining but not quite as bad looking, not much you can do about it but use the software mode (F9 while playing) which will make everything pretty slow.

is there anyway I could help like sending the developers the gs save? and i know what you mean about effects being missing, most of the dynamic lighting is gone and the flames are messed up too

You can try reporting it to the GSdx thread with a GS dump.

alright but how do I get around the file size problem

No need, thanks. We cannot fix this currently.
It's either software rendering or glitched hw, sorry.