I ran into a similar problem. I had multiple Excel files linked together, but only select formulas were not updating. I found that one file was trying to reference a combination of the SharePoint site and the old network folder structure. It was like it created it's own link (very strange). Looking into more I found and obscure formula with and old link that was over looked. Fixing this fixed all my other problems.
Had this happen in two different circumstances too. It appears that for some reason one incorrect formula/link can mess with everything else.
Hope this helps.