How to compare documents in Acrobat 9

I can't get the "compare documents" function to work. No matter what documents I choose, the message is always:

"Acrobat could not compare the documents completely. Do you want to see the report anyway?" If I say "Yes" it finds no differences, even though the documents are similar with incremental differences.

What does it take to get a proper comparison to highlight incremental differences?

I'm using Acrobat Pro 9, v 9.5.5.

Thanks

Mlbex100