Blue bars over screen even with skipdraw
Windows 8.1 
Pcsx 1.4.0 
i5 3350p @3.20ghz
RX 480 Factory OC 
8GB ram 

Issues: So iv been trying to play MGS 3 and iv been getting Blue bars over screen, when i change with F9 however i dont, but then in cutscenes and in codec, audio is slowed down aswell as picture sometimes. 

I tried skipdraw, i set speedhacks to balanced, i even messed around with all sorts of other options i found on internet, people had this problem but any of the tips given didnt help me, up untill yesterday, iv messed about in speedhacks and i had No blue bars without F9 and the cutscenes were fluid, like if i was actually on ps2, codec was perfect and everything. Then i booted up pcsx2 today started mgs and bam, everythings back. Im so dissapointed but i hoped someone here could possibly help me. 
Thank you and if i need to state some other stuff about it i will.

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Download the lateset dev build here and see if it fixes your issue:
AVX2 plugin is missing message shows up when i try to use the preconfigured GS plugin, but SSE2 lets me continue withthe installation

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Yes that's fine, keep going. Can you also post your GSdx settings as well?
You will need to use OpenGL and have the blending accuracy set to at least basic.
[Image: ref-sig-anim.gif]

I have started it up, set skipdraw to 1 and got speedhacks to 3, booted up the game and no fps issues or blue bars or slowed down cutscenes/codec so far. Maybe this made it work(the dev build or maybe even the gs plugin, could have been setup to the avx2 because iv had pcsx2 installed for quite sometime now just havent had time to play)? Iv had the same thing happen already tho it was ok after i messed around with it one day then the next day the problems came back, so if that happens i will try your tip Refraction, thank you both for help i really appriciate it, hopefully i can finally dive into it. Have a great day the both of you!

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