I've run a few of these tournaments before, and Competition Mode is NOT the same thing as playing a tournament game. Tournament games ALWAYS disable extra balls along with ALL free game wins (replay, special, match, high score award, etc.) Not so w/competition games.
To play a tournament game, the player MUST start from the installed optional "Tournament Start" button already mentioned, otherwise the score won't place among the tournament leaders. (Tournament scores NEVER go into Grand Champion/High Scores #1 - #4.) If the T/S button's wired properly, its lamp should blink (just like the Start button) IF AND ONLY IF enough credits are on the game to play a tournament game as it's set it up for. When starting from that T/S button, the very first thing you should see on the display is "Spider-Man Tournament" or words to that effect with "Tournament" in big block caps. (If there aren't enough credits, display will instead show "<X> Credits For Tournament Game.") At the game's end, display will say either "Sorry Player <X>, You Did Not Qualify, Please Try Again!" or "Player <X> - You Qualified!" followed by a 20-character name entry screen and then a PIN number entry.
If none of the above is happening, there are several possible causes:
1) Tournament is not started/active
2) Tournament is not configured properly
3) System time+date is not correct
4) Tournament Start button may not be wired in correctly (go into switch test and check it, make sure the button's coming up on the display as "Tournament Start" and NOT "Start Button"; I once came across an instance where a T/S button was crudely parallel-wired across the regular Start button so they both start a regular non-T game - idiotic ;D )
Hope this helps.