Shifting problem on two wheelset

Hi guys , i have two pair of wheelset.
The first pair i use for daily purpose and training , and the second one is a full carbon wheel i used for racing and as back up wheelset.
the problem is , with the first pair the transmission works perfect but when i use the second pair the chain seems to jump sometimes and the middle gear do not work properly.

Is possible to set up a perfect shifting with both wheels?