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.