This could be a side effect of Acrobat doing some "auto repair" upon reading in the file  (also see Unexpected & Unnecessary Popup "do you want to save changes to 'x' before closing ?").  What is triggering the auto repair has yet to be found out, though...

If you accept to save changes and then compare the newly saved version with the original one, are there any differences?  (use a tool to compare binary files, such as "cmp -bl ..." on Unix)

Update: for testing purposes, you could try to (dummy-)process the PDF file created via PDF::Extract using some other tool, e.g. the already mentioned "pdf tool kit":

$ pdftk original.pdf output fixed.pdf
[download]

This would fix anything that pdftk considers worth fixing...  Then check whether Acrobat is still exhibiting the undesired behavior when using this fixed.pdf.

BTW, you could also use pdftk directly to extract all pages:

$ pdftk sample.pdf burst
[download]

As hda said, an excellent tool — highly recommended!