They switched to a new hashing algorithm I think in response to the MIT paper debacle. Thus the same seed will now produce entirely different key pairs and addresses. Fortunately it seems that my problem (and presumably now your problem as well) will be addressed in a new version of the wallet with a "IOTA Recovery Tool" for recovering funds from old outdated seeds. At-least that is what I have been told. You came at a good time. I spent months worrying, if everything works out you will only have to spend a few weeks worrying. I'll link to the relevant post.