I'm having a little problem with Eclipse EE (juno) and CVS. When I'm trying to import a project from the server it only copies certain files from that project, and it looks like the other files do not exist on the server. As I'm the only one having that problem I suppose it means there's something wrong with my configuration or something.
Sorry, I don't use CVS so I cannot give a definitive answer, but here is what I would try:
a) Use a file manager to see what actually was checked out (I'm assuming that you are looking only at the Package Manager view in Eclipse, that sometimes is not that enlightening as to what really is on disk)
b) Use the CVS command line tools to check out the files and make sure that I get all of the files. (If this doesn't work you will need to get a CVS expert involved, might be permissions or something else)
c) Reinstall Eclipse (actually, you don't have to actually reinstall, just download the binary package again and unpack it in another location and run that one. Then open a new workspace and try the checkout again.)