After the PHP script finished running ALWAYS show the output tab. Now, sometimes it does and sometimes it doesnt.

I'd expect some thousands objections from the other PhpED users to be posted if we start ALWAYS showing the output tab. Indeed, if you stopped the debugger just because you found a problem and want to fix it, why would you need the output?
If, on the other hand, you're talking about something different, please find a way on how to replicate that and submit request to NuSphere Support. Forum can not help you with this.