If you use the autocalibration the AVr assumes that you'll have L+C+R+SL+SR, and that the SBR+SBL will be empty.
In your case you're connecting the SL to SBL and SR to SBR, so the AVR skips where you connected the speakers; but I'm sure it will test the SL and SR even if there's no spekaers connected ....Can you ear something when the AVr test the SL and SR??? ...I'm sure you don't, Right???
When you do it manually, you choose the spot that you want to test, Can you ear anything when you test SL and SR???
EDIT: The auto-calibration is a good starting point, specially if your AVR has a PEQ.