We fixed several bugs with identical symptoms during the v6 EAP and beta periods. This specific case was not tested by us as we had no evidence that it was any different from the other cases we knew about, and the EAP feedback that we got was that the issues caused by these bugs were no longer occurring, so there was no reason for us to investigate this specific case.
I have reproduced an issue with Unity 2.0, however. It only occurs if the target application is 64-bit and the profiler is in a line-level mode and seems to be due to an access violation in the .NET JIT. It's possible to work around the problem for now by changing the application target to x86 or by deleting the pdb or switching to a different profiling mode.
Red Gate Software Ltd.