Steps to reproduce.

1) Open a cmake project (in a dir called for example "myProject")
2) Close QtCreator
3) Rename the directory containing the project to have the same name, but alter the case (e.g. change "myProject" to "myproject")
4) Use the File->Recent Projects to open myProject (note the case is still the original case)
5) The project will build and run fine, but breakpoints will not work (the debugger console will show dNO LOCATIONS (YET) FOR BP for your breakpoints)
6) Close the project, then open it using File->Open file or project, and (because the case is now correct) the breakpoints will work

Might sound trivial, but took me a lot of work to figure out what the problem was!