I had to upgrade from 6.0R3.1 to 6.0R6 this last weekend due to the cpu spikes. I have been getting several rerports from users having their TS or RDP sessions freezing up. I saw where some were reporting this in Ver. 6.2 with Citrix Terminal Services, but didn't know if anyone else had seen it in 6.0R6.
A very similar issue to the one you describe was reported in 6.0, but was resolved with the fix included from 6.0R3 onwards. I have found no indication of any reported issues like this in your later version. I would strongly suggest you raise a case with JTAC if you are able.