I've been encountering this issue still (when not using the aforementioned fix). I found a more intuitive workaround than the previous answer supplied by fubarpk (thanks again!)
.... (normal startup properties here when blank project is created) ...
Sleep(100) // startup buffer
Print("Enter numbers to add together; terminate by entering a 0.")
Sync()
Sleep(2000)
This seems to always work, whereas before I would sometimes see the message, sometimes not.
Putting in the 100ms sleep buffer, I'm guessing, gives everything enough time to process before entering into the Print/Sync calls.
EDIT: I remove the [SOLVED] as I would like to see this fixed altogether. I'd be curious if I'm alone in this bug. As noted earlier, I have tested this on both Linux and Windows machines (two different computers) with the same 'bug'. This has fixed both machines problems. I should also note I'm programming on a burner computer, so it's not a top-of-the-line rig, which may be contributing to this issue.
I'm not entirely sure if this would be considered a bug still or not, but to those who may be suffering from the same problem, this is an easier fix than what I was previously using based off of fubar's suggestion. Figured I'd pass on my findings!