Lately I’ve been playing pokemon roms, specifically Pokemon Ultrasun; I never had any problem on my computer. After reviewing perhaps some movement within the Citra settings, nothing had changed. I desperately investigated, just as some are doing now. Turns out the Citra Nightly version is unstable so I managed to use an older version I found on Github and it worked for me. I hope can help you.
The version of Citra I am using: “Citra Nightly 1964”