Check to make sure the torque converter is fully seated into the tranny...if it looks like it's only about as far in as it would probably sit when bolted to the flexplate, it's not in far enough...I haven't looked at the hub on ours lately, so I'm trying to go from memory, but most have a flat surface machined into the side of the hub where it slides into the tranny...you have to get that aligned just right or it won't go in far enough...you should know when it's in far enough because it will almost look like it's in too far.
It can be a PITA sometimes, but at least you're not trying to do it from under the car with a crappy tranny jack that's so screwed up you almost drop the tranny half a dozen times <damn poorly-maintained equipment at the auto hobby shop>