I had this problem when I tried to install 0.99 from stable, and then purged it before switching to 1.9 from backports. Because /var/log/matrix-synapse and /var/lib/matrix-synapse weren't empty, they didn't get cleaned out. The latter held the sqlite dbfile, in which I'm guessing some bit of old config badness was hanging around. After doing another purge, manually removing those directories, and reinstalling, synapse seems to be starting fine for me now.
-- Kris Coward http://unripe.melon.org/ GPG Fingerprint: 2BF3 957D 310A FEEC 4733 830E 21A4 05C7 1FEB 12B3
