Ok found a way to fix it.
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FIX ISSUE: Fix for all emulators/clors (global fix)
1 - WINSCP to the device and goto the directory: /userdata/system/configs/retroarch/
2 - Edit this file: retroarchcustom.cfg
Look for the line that says: global_core_options = "true"
3 - Change the "true" to "false"
4 - Restart your system.
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FIX ISSUE: single emulator/core
1 - load up a game for the emulator
2 - goto the retroarch setting -> configuration ->
3 - where it say "Use Global Core Options File" set it to off.