Actually this is a behaviour which was recently "fixed" - but I prefer the "broken" behaviour. It has to do with the option to "close previous player" in the Start panel. At this point I can't remember whether this was enabled or disabled - probably disabled - but, once launched, the instance of Flash Player was left running and, with the next invocation of debugging, a new SWF would be opened in that same instance. It was annoying to have to manually close the previous SWF windows that tended to accumulate.
However, the current "correct" behaviour has the unfortunate defect of launching a new instance of Flash Player every time, whether or not the previous instance was closed or not (as per the option). On a heavily loaded system this launch could take 5-20 seconds which adds up quickly.
What I really want is for FDT to re-use the Flash Player instance, or to put it another way, the option be to close the previous SWF, not the player. If this isn't possible then at least go back (optionally) to the previous behaviour where the one instance of Player is re-used.