You could try using the Update ... option that brings up a dialog and then use the options to make sure the working copy has been set to be Fully recursive. This is the default behavior but maybe somehow you got a "sparse working copy".
As noted in the comment above, all of the work and logic is handled by SVN itself internally. Which is probably why you saw the same behavior when using the SVN command line client. I would expect Subclipse and the CLI to be consistent as they both are using the same libraries to do all the work.
Otherwise, I would just say the devil is in the details. Would probably need to see a lot more information about your working copy to know what is wrong.
If you are not already, I would recommend using Subclipse 1.8.x