Never mind, it's the right joycon not in place correctly. I may have mess it up using the jig I'm using. Moved it around and solve the issue. Update joycon work perfectly fine for me, no issue.
After updating to 6.0 and updated the joycon, the left joycon dont work anymore ONLY for homebrew. I'm running the latest hetake v4.2 payload with Atmospher (hetake) if anyone wondering. For all stock switch stuff, it work perfectly fine.