This is intended behaviour, Geany only allows one execute at a time and you may 
notice that the menu and toolbar icon changes to some form of stop or cancel 
icon which if pressed will kill the terminal, and so the running process (in 
case your new program gets into an infinite loop :) and when you close the 
terminal (after you have read the messages your program printed) the icon 
reverts and a new execute can happen.

However some terminal emulators circumvent this behaviour.  Instead of running 
a new window they open a new tab in an existing terminal emulator window and 
exit immediately, telling Geany that the execute is finished so a new execute 
can start but losing the kill ability.  

IIRC the KDE terminal emulator is one of those, and thats likely the behaviour 
you have been seeing in the past if there was already a terminal running.  But, 
if the terminal Geany runs happens to be the first one opened, it of course has 
to open a window and it keeps running, so Geany behaves as expected since the 
terminal process doesn't close immediately.

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