Had the same problem and found the solution thanks to a suggestion from user HOB on another thread that is linked in this one. Like many others here, I thought the problem to be due to a client upgrade, but actually it was a copy and paste issue. Version 0.4.8 allowed me to copy and re-paste a portion of my passphrase within the client's passphrase dialog box. Future versions of the client would not allow me to cut and paste within the dialog box. So I ran the old client, entered the passphrase using the old copy and paste method, and walla, there were my Nxt. Upon retrieving them I immediately transferred the entire balance to another account. Looks like I owe HOB some Nxt.
If you are having this problem, the best suggestion is to try and retrace your copy/paste steps exactly.