It sounds very much like you had a bad download.
try running a couple of things:
$ file old.pdf
$ xpdf old.pdf
$ gpdf old.pdf
$ pdf2ps old.pdf
$ gv old.ps
$ ggv old.ps
$ some-kde-postscript-viewer old.ps
$ cmp old.pdf new.pdf
If cmp says EOF, it means that the files are identical in the first N bytes, where N = minimum(sizeof old.pdf, sizeof new.pdf). Which would indicate an aborted download. Try looking at wget's resume download facility. Can you resume the download of the broken pdf?
In addition to the things I have suggested above, feel free to test out your favorite pdf viewers on windows as well.
I hope this enlightens you (a bit).