You can open a rtf-file in Notepad to examine the changes that Word 2003 makes in the new rtf by comparing it with the original rtf.
Then change your application to handle the new situation correctly.
An alternative would be to redesign the applications involved to use a totally different format (like csv or xml) in these files instead of rtf.

It might be easier to keep using an older version of Word to do the changes, but that's up to you.

Hope this helps.