Let me pose this:
Did you happened to check every pin out of the replacement ECU that it matched function and position to the original?
Also did you check the software and firmware revisions to see that they matched for operation?
The fact that you replaced the original ECU with another not specifically designed or programmed for your specific vehicle is a likely cause to your issue(s)
Not to mention what possible other issues you may have caused by installing a mismatched ECU