QGIS » QGIS Application

When saving a project on my QGIS 1.8.0 Lisboa (running on Windows Vista Home) where I did loads of layers editing, loadings and deletions, the qgs file is correctly created and can be re-opened with no problem.
However, the qgs file seems to keep trace of almost ANY layer I originally loaded in the project (including deleted layers, or multiple copies of the same layer). So much so, when opening the qgs file, layers get ALL loaded from hard disk and are at first listed in the layers' pane. When loading is finished, those layers that were deleted or duplicated disappear, leaving the Layers' pane as I left it when saving the project.
Strangely enough, I can still see them listed when using processing tools that let you choose from layers in use.

There appears to be no automatic tool to clean up the qgs.
Possible solutions I found: manual editing of the qgs file.
Transfer qgs file and layers files onto another folder (does not solve the duplications though), reopen it, accept to delete not found layers, save it again.

This very same problem has been raised before: http://lists.osgeo.org/pipermail/qgis-user/2012-September/019327.html
but cannot find it in this list.

I suspect this is linked to another issue I am facing: layers I choose to display are not always loaded at once. I often need to repeat the same operation again.
Any clues anyone?