I recently installed the latest version of Eclipse (eclipse-java-kepler-R, 22.214.171.12430919-0803) with the Force.com IDE plugin (126.96.36.199310181333). Everything was working fine until this morning, when it had lost the credentials for the project I was working on.
I could re-enter the password and security token, the plugin connected to Salesforce, but as soon as I closed the Force.com IDE settings on the project and re-opened it, the credentials were gone.
Logging into Salesforce, and going to the Login History of my account, I saw the plugin connecting just fine.
How can I get it to start storing the passwords again?