ID5 had lots of bugs when outputting the links between chapters if you use multiple files (book) method instead of single file for entire book. The links omit the file names. The fix is on Liz's site back around mid-late 2010.
Get used to opening and closing epubs to tweak files after export.
Necessary meta data will be missing and cover references need work to get them to appear on the shelf.
It's been a while since I used 5 but I'll dig up an old file and refresh my memory and point out the items needing to be fixed after export.