I've just installed 3.0.4 via Doctor and I can't save new files, but I can update existing files. Looks like a permissions problem on the folder but I'll have to find a Linux box to check.
You may find that one or more of the filesystems on the Touchpad is full. It's probably the /var or /var/file-cache filesystems. That's what I found. Once I cleaned that up, the problems instantly disappeared.
I wonder when they fixed it 'cause I doctored on Tuesday and just tested. I can save a file just fine; I just can't delete it from within QuickDocs. It reappears the next time I open QuickDocs. I can permanently delete it by opening up my file manager and deleting it there. I'm not doing another doctor until they get this all figured out. It is way too time consuming to get everything back to its original state.