The guy I took mine to is widely acknowledged as among the best in the biz for the 3.8. Anyone can make a mistake, though (I'm not saying he did, nor did he, but it's obvioiusly not impossible). In addition to finding someone competent you also have to find someone who will stand behind their work (which often is a lot harder than finding someone who is merely competent). He took the car back, pulled the motor, corrected the problem (which included replacing the crankshaft, bearings, etc.) and put the motor back in no questions asked. I think he charged me like $100 for some gaskets. I believe him when he tells me that he didn't find a specific cause of the problem. I think he's just a stand-up guy and erred on the side of making the customer happy rather than trying to blame it on something I did or installed.
I do agree that typically if there is any ambiguity at all the engine guy is going to try to place blame on the trans or TC rather than admit to poor machining. I'd say that if the TC and line pressures check out that the rebuilder has some 'splainin to do.
Jim