Go to View and choose Normal
Then go to Footnotes (at the bottom of the Window a pane will show up with all your footnotes)
There will be a drop down bar that lists the various components of the footnote -- choose footnote separator and make sure that it has no tabs or weird paragraph formatting applied to it
Then choose footnote continuous separator and right click and check out the paragraph settings and spacing
This is as much as I can help you, with out a Visual representation of your issue.
I am having a problem with the way MS Word is dealing with my footnotes. My dissertation seems to have too many footnotes and several of those notes are fully transferred automatically to the next page and therefore the long border-to-border line appears misplaced. I have tried working with MS Word 2003 and MS Word 2007 and happens the same situation in slightly different places. I have tried with the notes at the bottom of the page and at the end of the text without significant difference. I might place some of those notes in some other places to try to avoid the situation but not all of them.
I have been working long hours trying to solve this situation and have consulted to on-line forums without results so far.
Any suggestion?

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