Available Updates for Remote Desktop Services (Terminal Services) in Windows Server 2008 R2
Latest BaseCSP.DLL (as of April 2012):
You may wait for up to 30 seconds when you use a smart card to unlock a computer that is running Windows 7 or Windows Server 2008 R2
Latest Winscard.dll (as of April 2012)
A program that requires you to use a smart card stops responding in a remote desktop connection in Windows Server 2008, in Windows Vista, in Windows 7 or in Windows Server 2008 R2
...and make sure you're at SP1 on the W2k8 R2 terminal server.
...also make sure you create and set FilterCSPCardCacheByTSSessionConnectTime to 1 – it is by default 0 or not present (this is read by the BaseCSP.DLL component).
See also http://blogs.technet.com/b/instan/archive/2011/03/24/smartcard-redirection-diaries.aspx for other aspects.