One workaround which may suit users who are mainly off the corporate network is to enable VPN login before Windows login, in the options of the Cisco VPN Client. This should help preserve homedrives and allow login scripts. Of course it's more annoying for users who mainly log on at the office.
Another suggestion I had heard is that a particular application may cache its name resolution attempts, even after you have flushed the DNS resolver cache, so that open window of Explorer might believe that serverx is not reacheable until you restart Explorer, howver I have not been able to confirm this.
I have experienced this problem, it is frustrating to trouble-shoot because users are by definition offsite when they experience it. Another factor which complicates a split tunnel configuration is that if your internal domain is company.com you way well have external public-facing DNS for www.company.com etc - when your user tries to resolve the internal fileserver.company.com they'll get an authoritative answer from the external DNS that "fileserver" doesn't exist.