is it just happening on pokemon green? same issue on red/blue?
check framerate setting, change max fps (i left it at native)
check with audio/video sync check/unchecked.
change video render (open gl old, or software or whatever else is there)
check your task manager, last time i had problems something else was using my memory and CPU
i'm assuming it's not a mGBA issue, i'll check on my end
(after check on my end)
yeah it's not happening to me when i tried it here, i have SGB borders on too (it didn't change without it on GB only) i'm also tried with 2x speed and unlimited speed no lag at all.
so i'm gonna post screenshots of any settings that i think could help.
check version number too, in case it's not updated to now.
I hope something here helps
also try a full PC restart, i know it's dumb but you never know what crap your PC does
random thought, is the game in a zip file? highly doubt a GB game would struggle to load out of one, but i'm narrowing options down.