ImageMagick - Convert multipage pdf to animated gif
The following command worked well for me from a paper PDF I've worked on. The only difference from your original command is deactivating the alpha channel:
convert -alpha deactivate -verbose -delay 50 -loop 0 -density 300 paper.pdf file.gif
I'm using Version: ImageMagick 6.8.3-3 2013-02-21 Q16 http://www.imagemagick.org and homebrew.