The short answer is that jAlbum keeps track of what processing is needed for an album using the control files in the image directory (things like the .info file). If you have two different projects, but sharing a single image directory, it has no way of getting it straight.
Open each of these projects in jAlbum, and take a look at Settings > General > Image directory. If both projects are pointing to the same place, you will continue to have problems.
This is not to say the each project needs to have its own copy of the source images. The projects can just contain links to the source files, rather than keeping copies of them.
Sorry but it's not a response to the question.
We use two album for precise reasons, on mobile we want small picture, fast loading on computer we choose other picture size, another behavior ...
It's the same skin but with other parameters.
You could use jAlbum’s variants to generate images of both sizes, within a single project. The browser will load the small or larger image, which ever is the best fit for the device.
As Jeff says, linking to the images would avoid problems. There is a tool that will convert a project to a mirrored project.