I have same problem, My fortigate is 310B with firmware 4.0 MR3, Client OS: XP/Win7.
If the Split Tunneling is enabled, the client often can not resolved intranet dns, user have to logout and login many times and check if the dns is resotred to normal. i found the client has two dns server when the ssl vpn is connected, one is for internet, another is for intranet (ssl-vpn), and client use the internet dns server somtimes, and use the intranet dns server somtimes, i can get the correct ip if use the command " nslookup intranethostname" ; but can not get the correct ip if use the command " ping intranethostname" sometimes, it return " Ping request could not find host intranethostname.com. Please check the name and try again" .
If disable the Split Tunneling, because the client can not connect to internet dns server, it has to use the intranet dns server, and all dns can be resolved successfully.