What happens if you accelerate hard in third? Does it feel worse, like it's skipping?
Motorcycle transmissions are called constant-mesh and it would be super rare to break a gear. However, gear pairs are held together by pins in holes (dogs) that can have their edges wear off and skip like you're describing, and yes, it would only happen in one gear.
If thats the problem and you continue to ride it, it will cause pressure on the shift fork and overheat and wreck it too.
The only way to look at a transmission in an XB is to remove the engine and split the case.