Ok thanks to your reply I think I figured out what was going on. Since I was mixing "switching" with "opening" I had some projects in other main windows, and, as you mentioned, having a project in a main window, "ST window", removes it from the switching window. From my point of view it was chaotic.
I didn't even realize there were multiple ST windows open. Boy, those are a terrible idea. alt-` between those windows is just disorienting since there's no clear indicator of what project it actually contains. I see that ST3 is adding a "switch project" menu item. Maybe this will make it a little more obvious as to whats going on.
My opinion, for maximum clarity, only allow one project at a time to be open, switching is just so easy anyway, and I cant picture myself needing two projects open side by side.