Hi
A little bit confused because you say you have 3 systems but then say both are running Vista Premium. Also your text is a little confusing because if you can remote logon you should be able to see all your files there - just that they aren't remotely accessible via a file system operation?
If I assume you are using Windows shares then these will be created via the local server service. You could run up services.msc via a remote logon when you have issues and see if it (and the workstation service to be sure) are started. A good way to check is to sort all the services by Startup Type and note down all the ones that should be set to start automatically but that are not started (indicating a potential problem - some services only start up when you need them but on a workstation OS is this less common.)
Another thing to do is have a look in the windows event log (eventvwr.msc from Start->Run) - see if you have a bunch of red errors in the system (and maybe application) that might give a clue that you can run through your favourite search engine.
Of course, you haven't updated your AV / Spyware client have you?!? For example, see http://www.experts-exchange.com/OS/Microsoft_Operating_Systems/Windows/Windows_Vista/Q_23631054.html
Hope this helps a bit
Cheers
Drew