From a fellow mac man to another...
i join my tunes using a program called iTunesJoin which i downloaded from the apple website a few months ago. it's only a 30-day trial to start with but u can buy it for just a tenner! it joins all tracks you've highlighted together into 1 longer track, eg. side 1 & 2 of a set into 1 track... as far as i know it's only available for mac & it'll appear in the drop down menu for iTunes as a script logo. Works great for me!
i think it was somewhere in the audio downloads section of the apple website, or you can search for iTunesJoin within downloads.
Hope this helps