I'm all for consistency. The easiest way to be consistent is to follow the rules as they appear in the rule book. The rule book says that if an inning ends and time is left- any amount of time- then you play the next inning.
This isn't an "ASA thing" versus an "NSA thing". I've worked in both associations and have seen umpires handle the clock every which way you can imagine. Neither association specifies any certain kind of timing device, but they both have the same rules about when an inning ends and when the next one starts.
It is an "individual thing", in that ten different umpires might have ten different methods for keeping track of the time. But what else can we expect? The rule book does not address the timekeeping device used or how it is interpreted, because this sport isn't designed to use a clock! With no printed guidelines and no rule covering timekeeping devices, how could you ever expect consistency? It is left up to each individual umpire to come up with his own method of keeping time.
My personal observation has been that I saw much more abuse of the clock in NSA games, with umpires routinely cutting off the last few minutes of games and "cheating" the teams out of the final inning. But that was just my own experience. When you're talking about hundreds of games and hundreds of umpires spread throughout the state, it's going to pretty much be the luck of the draw on how this shakes out. It's easy to believe that your experience has varied, but if it did it was just random luck, not because one group or the other has different rules or training on how to keep the clock.
When working a timed game I use a countdown timer, preset at 75 or 80 minutes, or whatever the time limit is for that game. The ASA rule book says to start the timer on the first pitch of the game. For most tournaments I work, the TD's tell us to start the clock at the end of the plate conference or on the catcher's throwdown when warm-up pitches are completed. (So, most tournaments are instructing their umpires to shave some time off the game right off the bat, whether the teams realize it or not).
And, if there is any time left on the clock when an inning ends, I tell the teams we are playing another inning. That is what the rules say to do and that is being consistent!
Of course, I wasn't the tournament director for these games. If I was, I can't see how you could uphold a protest for letting a game continue with time still on the clock. That is exactly what the rules tell us to do!
I would uphold a protest for ending a game with time remaining. The game that was ended with five minutes left really did shortchange the teams and violate the rules. That's the one you should have protested!