First, the "new version available" alert will continue to show up as long as a) there is a new version available, and b) you haven't told it to stop alerting you. Version 2.1 was released last Friday, but it was quickly followed up with 2.1.1 on Saturday, and then a 2.1.2 on Monday. So, if you don't have version 2.1.2 installed, you don't have the latest version. You can see what version you have by viewing the "About" dialog. Press the "About" button on the Game tab, or right-click anywhere and select "About The Tournament Director".
Second, I think Tim understood your confusion better than I did. The "Don't Scroll Seating Chart" option is meant to stop the Seating Chart page from automatically _scrolling_ up and down to reveal all of the tables, if you have enough that they don't fit on the screen. I think, as Tim said, you're trying to make the screens stop switching from the Tournament page to the Seating Chart page, etc. There is a question in the FAQ addressing this:
http://www.thetournamentdirector.net/faq.html#faq21Rebuys and Add-ons are traditionally done via a Hotkey. By default, the V key is used to rebuy players and the B key is used to add-on players. Pressing one of those keys will bring up a dialog box and allow you to select players to rebuy or add-on. You can also add a button to the Tournament page to accomplish this (via the <tdbutton> token). You can also right-click on a player's name (on the Tournament, Player Rankings, or Seating Chart page) to get options for that specific player, including buying-in, busting out, rebuying, adding-on, and undoing any of those.