What does "Duplicate INDEX entry" mean?

[Jason Dusek]

Every so often I run make index, and I always get the following output:

   Generating INDEX-5 - please wait..Warning: Duplicate
   INDEX entry: freeciv-gtk2-1.14.1
   Warning: Duplicate INDEX entry: mod_jk2-apache2-2.0.2
   Warning: Duplicate INDEX entry: mod_rpaf-ap2-0.5
    Done.

What does the warning mean? How do I get these warnings to go away? The index 
builds fine, but I really don't like the idea of leaving these warnings hanging 
around.
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