I'm seeing a lot of issues lately with ecu replacements. Many of the ECUs available come in from Euro markets as secondhand units. That's no issue, as I do the same, but what happens is that guys simply align these boxes and leave it as that, because the car starts. They don't bother loading the correct software on these ECUs specific to our region so the car never runs correctly after a replacement.
Case in point, the other day I had a 330d here. The replacement ecu came from a 730d. The guys simply aligned it and the car started, so they left it as that. Climate control didn't work, cruise control didn't work, there were lots of faults related to exhaust back pressure monitoring (which isn't monitored on cars sold in SA) , etc. And you don't simply update the software, in this case, through obd, it needs to be done through BDM because of power class issues.
I'm not saying it's the issue in your case, but it seems to be a common issue nonetheless. Cheap tools gets you a starting car, expensive tools and experience makes sure the car is perfect after an ecu replacement job. During the rainy season I was doing an average of 40 to 50 ECUs a month, with a 100% track record...
If you're in the East Rand area you're welcome to pop past so I can at least have a look to see what's up.