Performance drop from 4.6 to 4.6.1 on overclocked RPi 3B

[MVivi]

Hello!
I installed version 4.6 of retropie on my overclocked Raspberry Pi 3B, and everything was working perfectly. Today I updated to version 4.6.1 from the retropie-setup menu and I got the audio issue described in the pinned post, which has been solved following the steps. However, I tested the performance by running Mario Kart 64, and it runs slower than in version 4.6.
Is it possible that the overclock settings -in config.txt file- are being ignored? Is there any other possible reason?
In case they are useful, these are my overclock settings:

total_mem=1024
arm_freq=1300
gpu_freq=500
core_freq=500
sdram_freq=500
sdram_schmoo=0x02000020
over_voltage=2
over_voltage_sdram=2

Many thanks for your support.

[quicksilver]

@MVivi which emulator specifically did you use to test Mario kart 64?

[MVivi]

Sorry, I forgot to tell that. I'm using mupen64plus, and I've tried all three plugins with the same result.

[quicksilver]

@MVivi did you also update mupen64plus?

[MVivi]

I chose the option to update all installed packages, including system packages.

[quicksilver]

@MVivi A couple things to check. Make sure that you are not running in 4k display mode. Go to raspi-config and set a lower resolution like 1080p. Also go to /opt/retropie/configs/n64/mupen64plus.cfg and make sure that in the gliden64 section that the hybrid filter option is disabled.

[MVivi]

Unfortunately no success, I had already disabled the hybrid filter, and lowering the resolution even to 720x480 had no positive effect.