This may be of help to you or it may not..here goes-As far as I am aware and I got this from speaking to my son who is a motor vehicle technician [they were mechanics in my day..] your ECU needs to be hooked up to what is known as a TECH 2 diagnostic unit and this will interogate the ecu and basically spill its guts [for want of a better phrase] as to the root cause of the fault.Also you really needed to install the ECU from the vehicle that the recon lump came from as I believe that they come as a matched pair from the factory.In other words your ECU is trying to read a strange engine [if that makes any sense..]
As an aside there is a chap who takes out a full page ad in the autotrader magazine who claims to be able to reset ECUs etc but I have no knowledge of him but he might be worth a go.Best of luck!!!!!!!!.