I think the references are always like that - it has to be so you can link workbooks to data. In fact I think that the whole path is really there - excel just displays what you need to see.
How I have got around this is to simply do a global search and replace in the new workbook swapping the old workbook name - not forgetting the [] - with nothing (in teh dialog box for the new text dont put anything at all). This makes all the references point to the current workbook.