Normally, I am able to stream at 3000 bitrate with no frame drops. However, when streaming Super Meat Boy, even at 100 bitrate I drop around 70 - 80% frames. I tried lowering video quality, setting bitrate higher, changing encoder, twitch server, CPU usage preset, in-game quality settings, doing both game and window capture - none of these worked. Looking into task manager, neither CPU, nor memory or GPU seem to be near 100%. Also tried streaming other games to make sure it's not temporary network issues, and it worked fine.

Does anyone know what might cause it?

Meatboy can cause these problems and I'm afraid there is no simple fix to that issue. It looks like you have tried many things so I don't have many suggestions. Things you could still try is using GPU encoding in OBS and rivatuner: https://www.speedrun.com/smb/thread/tw32f