Intrinsic matrices in stereo camera calibration
You are correct: during stereo calibration the parameters of both cameras are optimized simultaneously, which is why you get the discrepancy.

When you calibrate a single camera, you are minimizing the reprojection errors  from projecting the checkerboard points into that one camera. When you calibrate a stereo pair of cameras, you are minimizing the reprojeciton errors from projecting the checkerboard points into both cameras. Since you are minimizing different functions, the results will not be the same. However, the difference should be small.