Safari 3 won't open PDF files

Since installing the OS 10.4.11 update, I've been having problems with downloading PDFs. When I try to download, I get a blank, all-gray window, with no content. This does not happen with PDF downloads from all sites, but for a very frustrating majority of them.
I had a similar problem with the public Beta version of Safari 3 also, though that version crashed every time I tried to download a PDF. De-installation and re-installing Safari 2 solved that issue, but that seems to be more difficult since Apple packaged Safari 3 with the OS update.
I've been reading through some of the problems others have had, and the proposed solutions, and can say that I have no helper apps or plug-ins to interfere with things.

Still no good after repairing the disk (no repairs necessary, apparently), and trashing the Safari preference file.
I've been exploring to see when the problem occurs. Seems to be specific to one large set of sites - scientific journal publishers (e.g. Highwire Press), or databases (e.g. JSTOR), or many articles found through Google Scholar. Other PDFs from various sites seem to come through fine, but journal articles come through as a solid gray window (most of the time). I have noticed that the PDFs that come through okay transition through this gray window, sometimes for a second or so, before the PDF comes up.

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