Sorry I can't help you as I am having same though even worse problem. The following search returns nothing, however each separate part returns tasks.
list:reference AND list:waiting

I am just starting to use SmartLists so hopefully someone will enlighten us about any gotchas in the proper syntax for query. I assume that you have seen some of the syntax rules that can be seen when you go click the "show search options" link below the Search box and then on the subsequent page click on the Advanced Search link.

Have you tried to change the order in which you type the 3 lists? Is it still only tasks from the first 2 that show up? It really sounds strange, hopefully just a spelling error.

Sorry for my previous answer, the reason is the incorrect use of AND. In this case, you'll want to use OR as that will catch tasks in list1 OR list2 OR list3. If you use AND you'll only see tasks that exist in all the three lists simultaneously.