Yeah Charleski is correct.
Is isn't an iBooks bug though, it a CS5 issue
All the links will work going there, but the return trip back all the links will be broken.
you can run a search and replace on the xhtml files to fix this though, it only take a few minutes.
For example I had one with hundreds and hundreds of footnote/endnotes. all the links from the text to the "notes" worked but the going from the "notes" file back to main text were broken...
you just need to insert the correct xhtml file before the #
href="filename.xhtml#dried-wild-mushrooms-anchor"
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