Just posting for posterity in case someone else has this issue. I re-flashed it with https://github.com/Zerabosk/GB303 version and it solves the issue.

I want to use my LSDj as master and send data to the GB-303. I set the GB-303 to LSDj slave (I didn't pick this nomenclature!) And put LSDj to sync mode: LSDJ. When I hit play. They start together but the GB-303 is going much slower. Even if I set both at tempo 145 and press start at the same time, the GB-303's idea of what tempo 145 is seems a lot slower than LSDj.

I am using a GB Pocket and a modded Gameboy Color. I also tried Gameboy Color with Super Gameboy 2. I also tried swapping which device is master or slave, same results all around. GB-303 is on its own proprietary cart and the LSDj is on an everdrive.