It is a complete crapshoot my friend. Since auto-sense/auto-negotiation is not a true 802.1 standard each vendor interprets it different, and even WITHIN the vendor product, there are difference between families. We have dozens of Cisco switches that connect fine with dozens of Nortel switches just fine, however, dozens wont as well. If you are sure you don't have a cable problem...aka you arent using straight through cables on MDIX to MDIX ports, or poorly terminated cat5, then yes, you will potentially have to manually configure ports prior to connectivity.
I hope this info is helpful.
-HH