I have noticed this also. Sometimes it seems to randomly select an entirely different AMS slot. I had a yellow PLA job (in AMS slot A1) get pulled from the other AMS slot B4. Both were set to Bambu PLA basic, but were properly set to different colors. I had resynced and specifically set the object to use A1 yellow.
This never seemed to happen with Studio before the update to 1.10.1.50.