Before 1.6.0, CPS1&2, NEOGEO games are almost running in full speed (59.8338 fps). After updating to 1.6.3 & 1.6.4, all game speed often drop below 50 fps. I also cannot load Violent Storm with MAME2003 core. On PSV, everything seems fine on the newest version.
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I have also noticed that the latest build has problems, I was getting most of my games at 60fps however there has been a massive drop in quality since the 6… versions have been released with FBalpha and PCengine cores suffering for me at least.
I was getting 60fps from turbografx/Pc engine CD roms on 5.1 but now its like 45fps I reverted back to 5.1 however I couldn’t get my turbografx / PC engine CD roms back up to 60fps im gutted as I didn’t save a back up of the old working build 
That sounds terrible! Maybe I should wait before I get the latest version of RetroArch! I can’t even copy the files! It says it needs permission to copy the “cores” folder!
We might have figured out the problem.
As soon as I hear that this fixes the problem, I will probably release a quick new emergency release.
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What about my problem then?!
I have even made a post about it!
Your issue might be a simple enduser oriented problem that you can probably get an answer to on jailbreaking / homebrew forums. Could be a simple file permission issue or whatnot.
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I have an question! Did the nightlies for RetroArch 3DS update with the fix?