Presently, I can't save files from Mail anywhere within my Home folder. I also can't save a preference file from another app. When I try to install a Mozilla plug-in, I get an error. However when I check file permissions from Terminal and Finder, I see that I am the owner of all directories with read/write permissions, and all files seem to have the same. I was able to download and install some applications in the Applications folder, by dragging them to the folder.