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Hey I am new to PCSX2 emulator so I am sorry if this is a FAQ but whenever I increase the internal resolution lines appear in the dialogue box for some games. Is there a setting to change or a quick fix for this? Any insight into this would be greatly appreciated, thank you.

Try enabling hw hacks in gsdx and using the "align sprite" option.

"Round Sprite" is another option you could try if the former doesn't work.

For some games those lines are unavoidable as they stem from using a resolution higher then native. All you can really do is get use to them.