I've been developing Join Together since 2004, when it began as just a simple AppleScript that automated the process of using QuickTime to combine the files of selected tracks into a single file. Later, I added the Cocoa interface and ability to chapterize with Apple's "ChapterTool". Well, "ChapterTool" requires Rosetta to run and Apple is discontinuing support for Rosetta in OS X Lion. That means that Join Together will be unable to to use "ChapterTool" when run in Lion and there really isn't anything I can do about it. C'est la vie, to put it politely.
There are other apps that perform similarly (and better), but I know that Join Together is a favorite among a small number of Mac users (it was designated a Mac Gem by Macworld in 2008) which is why I have continued to maintain it. Therefore, I will be releasing an updated version of Join Together that side-steps the chapterizing options when run in Lion. However, these options will still be available when it's run on Snow Leopard operating systems.
Look for the update within the next few days.