After googling a bit, I found that this may be related to changes in the fontconfig package. I tried making manual changes to /etc/fonts/fonts.conf to comment out the rules that substitutes Nimbus for Times, but I still have this problem.
** Also affects: fontconfig (Ubuntu)
Importance: Untriaged
Status: Unconfirmed
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pdflatex not using correct fonts
https://launchpad.net/bugs/51508
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