I can think of two reasons this may be happening:
1) CRC or checksum calculations at the start vs. end of the tag ID (vendors may implement this differently) but it sounds like you've already investigated that
2) The readers are configured to read different areas of the tag. For example, are you sure you are getting the tag ID in both cases? For passive UHF RFID Tags, you might be configured to read the TID Serial # vs. EPC. For HF MiFare readers, perhaps you are reading a data bank on one reader and the ID in the other. This is a long way of saying, are you sure both of your readers are actually configured the same way?