Subclipse has many problems like this. It works 90% of time, and then it just DOES NOT work as it should! I am using subclipse, since it is very well integrated into eclipse, and when I have problem or some bigger moves needed in svn (like merging some branch) I use Tortoisse.
I had the thing with directory like you. Then I just run the TortoiseSVN like @luiscolorado suggests, and it helped. Tortoise is so great tool (it has many great features for diffing, applying patches, getting patches and so on.).
Today I had a problem when I have removed a file, and someone had changed the same file! Then subclipse shows conflict (up to this point everything is ok), so I wanted to revert! But then the revert button is missing (disappears when inconflict mode!) so I have to do merge, and merge does not work, throws some kind of error. I didn't bother to read (maybe I should read and file it as a bug to subclipse maintainers ;-(), I knew the tortoisse will work, and you know what, it worked. There was a REVERT option.
So @Tom Brito, try command line, try Tortoisse, and then you can look at the subclipse changelog and file a bug. I think that subclipse just forgets to show us some directory changes and updates (or it is designed not to do it?), but I may be wrong.