Worse N64 performance after updating stock 4.6 image

P-Rock

This past weekend I updated my raspberry pi 3 from retropie 4.3 to 4.6 After the update I booted up Mario Kart 64 (my most frequently played game) and noticed that my performance was noticeably worse than before. With 4.3, I was able to run it smoothly at 1080P screen resolution and frame buffer with the GLes2N64 emulator. Now performance was a stuttery mess with the same settings.

As part of my troubleshooting procedure, I reverted back to a totally clean 4.6 image and tried Mario Kart with a 1080P video mode/framebuffer and GLes2N64 . To my surprise it ran as smoothly as before. However, it didn't seem like the framebuffer resolution was getting set properly--the image filled the TV screen (so I think the video mode setting was correct), but the game looked like it was being rendered at some lower resolution--my guess would be 640x480 or 320x240. After running this test, I updated my system using the retropie update script. I'm not sure. After an update and a reboot, I started Mario kart again, and the stuttering was back. So my questions are:

Why is Mario Kart not getting rendered at 1920x1080 in Retropie 4.6?
Why did updating with the retropie script lower my performance? FWIW my audio was also stuttering, so I'm wondering if this has anything to do with the audio issue mentioned in the pinned thread.