Hi da_jane!
This could be due to the fact that the pages with the same size will be merged and if for example a single page has some extra lines extending the "normal" page area this extra lines will be very transparent and hence not easily recognizable on the merged image. This is sometimes the case with scanned pdfs.
OR
its a bug. In this case I would ask you to send me the pdf to
gerhardtt@gmx.at and I will have a look at it.
Greetings,