The best thing to do is to post your offending code here (with some comments as to what you're trying to achieve within), so we can review it It's difficult to second-guess what's happening otherwise as my crystal ball is on the fritz...

When saving to EEPROM, you must save the highbyte and lowbyte of the WORD individually into separate addresses. Then when reading back, you also have to read the highbyte and lowbyte back (again as two operations) to reassemble the word.