It's a fair point, and eventually we did "fix" it, but not until 7.0.
The reason why the problem exists in the first place is that the standard I/O window, which receives the output (or the console window), is part of the process of the debuggee, not the debugger (CVI). When the debuggee's process terminates, the window has to be destroyed. This was only an issue in versions 5.5 and 6.0, since prior to that CVI used to debug user programs in-process, in which case we could keep the window around as long as CVI was up.
Eventually we got enough feedback that this was a problem for us to do something about it. Sorry that it took so long 🙂
Luis