I also had this problem.  (Related topic here: https://bitcointalk.org/index.php?topic=812737.0)


SITUATION:

I tried restoring a wallet using those twelve words I'd written down and it came up empty!  This was a terrifying experience.


TECHNICAL:

I created the wallet 2-3 years.  I think the version was 1.9.8, though I'm not certain.  Now, I'm using 2.5.2.


MY COMPETENCE:

I've taught people to do Electrum wallet backups at a local meetup, so I'm pretty confident in my abilities.  I also restored the wallet successfully about a year ago. 


RESOLUTION:

I had a digital copy of the wallet saved on my super secret flash drive.  I renamed it from "electrum.dat" to "default_wallet" and my great relief, it opened and all my bitcoins were there.


DEAR DEVS:

I've recommended Electrum in the past and want to continue recommending it.  If there's any information I can provide to you so that you can trouble shoot this problem, please let me know via PM.