PDF is bad on web site

I created several PDFs from InDesign CS5 and checked them in Acrobat 9 on my system; all fine. I uploaded them to my publisher's FTP server and they put the PDFs on the web site that accompanies my book. When I open the versions on the web, there are extra spaces between letters in the middle of words. I downloaded one of the web files and checked the font embedding (seems OK). I also tried looking at the files with two different PDF viewers; same problem in both. I checked the orignal PDFs again, and they are indeed correct.
I am totally stumped and will appreciate any help. See the image below. The text is in Latin so I circled the inappropriate spaces in red; these should all be single words. The font in use is Myriad Pro.
Thanks -- David

Thanks for the replies. I did use binary mode when I FTP'd the files.
Comparing the two documents shows differences (see screenshot below). If I understand correctly, a PDF includes a low-res graphic version of each page as well as the underlying text. So the parts that are highlighted in red and marked as changed belong to this graphic, right? If I uncheck "images" at the left, no differences are reported, i.e., the text is unchanged.
But when I view the PDF on the web site, I can enlarge it to a high level and it's still sharp. So the graphic version is not being used for display; the text is rendered using the actual font, right? Also, the boundaries between changed and original images sometimes correspond to places where there is extra space, but often do not. So I'm still in search of an explanation.
David

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