Character set encoding can be the source of the problem. But if this is the case, we can't do anything about it without knowing some internal details of this file.
I searched for a tool which can dump internal details of XLS file in a useful format but I wasn't been able to find a good one.
Some tools can dump binary representation of different workbook parts but I don't think that comparing binary data will be helpful because of the difference in the size of original and resaved files.
There is one tool which shows internal structure of a workbook in a human-readable way - POIFS Browser.
But it doesn't seems to work quite well - some elements are displayed in the list but you can't view their content. And there is no way to dump elements list.
Another problem is that it's hard to describe which data to look for (since XLS file is created with third-party software, it can have a slightly different structure and format). But if you would like we can look at this file together through Skype or WebEx.