This could be a side effect of Acrobat doing some "auto repair" upon reading in the file...

Having tried PDF::Extract on some randomly selected pdf files, I find that its output is badly broken -- in particular, the 'xref' table is a mess.

When Adobe Acrobat (Professional 8.1.2) read the output of PDF::Extract (which it wasn't always prepared to do) it would offer to save changes on close -- and the result was a cleaned up file.