It turns out my "fix" is not a fix at all. Uploading PDFs works on the computer I tested the fix on, and not on the computer I first tried it on, regardless of this change.
I see the mime type which squirrelmail uses comes from $_FILES which is set by the uploading browser. Why the same version of Firefox on the same version of OS X has an issue on one system but not another nearly identical system, I don't know (one uploads PDFs as application/pdf and the other as text/html, confirmed via a test form). David.
