Yes, it does matter when the protest was made, because that's the point where the game will be resumed, in this case, the bottom of the 3rd inning.
The coach of Cuddy's did indeed inform the umpire, the first time the 10th spot in your batting order came up.
Then once again in the bottom of the 3rd inning and that's when I received a phone call.
Again, we are all moving forward with what happened, but these posts that I wrote gives the teams in the league a better understanding of how to avoid the same situation again in the league.
Here's a reminder to all teams in the league, that a 10th player can be added at anytime (even after a team has gone through their lineup once or multiple times) and that when a 10th player does arrive at a game, he MUST be entered into the game at that time.
If a team refuses to enter a 10th player when he arrives into the game, then the player becomes ineligible to be used as a substitute at a later time in the game.