This bug was reported to the Debian BTS.
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=367612

"/usr/bin/evince-thumbnailer, called by nautilus to generate thumbnails of
evince-supported documents, generates PNGs with RGBA channels. However,
new nautilus behavior does not put frames (border & dropshadow) on
thumbnails with alpha channels. This seems to be intended so that icons
and other pics which look nice on any background will look nicer. The
types of documents supported by evince, however, usually do not look
good on any background, specifically white pages on white background.

What happens:
Thumbnails of PDFs, etc. appear in Nautilus as tiny text floating in the
middle of nothing. There is no border to suggest the edge of a page.

What should happen:
evince-thumbnailer should generate only RGB PNG thumbnails.

Test/workaround:
It's possible to go into ~/.thumbnails, open the thumbnail in question
in GIMP, apply a Flatten Image to convert RGBA to RGB, and Save. The
thumbnail now renders correctly (with frame) in Nautilus."