If you want to deploy Xenapp6 on Windows Server 2008 R2 SP1,  you need install this hotfix and it is named XA600W2K8R2X64026.

It can be dowloaded from: http://support.citrix.com/article/CTX127360

Before install you should disable UAC: http://social.technet.microsoft.com/Forums/en-US/windowsserver2008r2general/thread/7b7476ee-539e-4aeb-995c-65e3cf57f817