Corrupt links after upgrading to 2007

I have several users who have found that links to other workbooks are
incorrect after a recent upgrade from Office XP to 2007. The source
workbooks haven't moved or changed and the links can be corrected.
For the moment everyone is using Excel in 97/2003 compatible mode, so I was
hoping to avoid any issues relating to the new format.
Not all links are affected. Some have lost part of their path to the other
file, others have had the correct sheet name removed and substituted with an
incorrect one.
Anyone have any idea of what might be causing this?