tarazed, thanks. Like you, I've found that using the option to automatically remember running applications is unreliable. Also, when you turn it off, it deletes the saved session (unlike GNOME2, which kept the last saved session). As I used this feature to set up my default working environment (an open terminal window), not to remember what I was last doing, this isn't helpful. However, I've found that using the other tab in gnome-session-properties to add a startup program, and using the gnome terminal --geometry and --working-directory options gives me what I want, and appears to be totally reliable.
I think we need to start a MAQueia thread to capture the useful information from this thread, as it has got a bit lost amidst the advocacy for/against GNOME3.