Not sure how to troubleshoot this problem. I have an IntelliJ11 Ultimate Edition, used in 64-bit, which I use for a PHP project with several modules. This project has 3 modules, but every time I close Intellij 11, when I open IntelliJ again, I find that the module has disappeared.
Steps that I have used to add this PHP module:
File->Add Module->Create Module From Existing Sources and I select the directory with the module.
or
File->Add Module_>Import Module from IML (I've tried importing the module-level IML file for the disappearing module), but regardless of which I try, I still fail to retain the 3rd module on the restart of my IntelliJ and I end up having to add the module again. (If I added the IML, I get a message on the restart that it cant add my module because the module is already in the project).
The workaround that I came up with was to import the root IML file into my project, and thus have access to the entire directory tree in my project view. This isn't ideal, and frankly it's a bit disappointing from such a good product.