Hi salviati, welcome to the forum!
If you have used the "Compare WAVs" function of EAC to do the comparison, can you post here the results?
If the mismatches are at the beginning or at the end of the two files, it is probably a problem related to read offsets (if you don't know what offsets are and/or want to know more, visit The Coaster Factory and read "The truth about offsets"). In this case, for your purposes you can ignore them.
If the mismatches are in the middle of the file, then you should be concerned about that... On SATCP you can find very good tutorials about EAC configuration and fine-tuning.