Occasionally I encounter similar problems. On occasion the project.pro.user file gets corrupted which
can cause undesired behavior.
In that case, removing the build directory is not enough. This is because clean essentially removes the build files. But if the project configuration is telling build to clean/compile things the wrong way, it makes sense removing it would not help. Removing the pro.user file should, though you will need to reconfigure a little (unless you want to check through it which is a pain).
I found just deleting it and letting QtCreator regenerate it fixes most problems. I have yet to need to remove the .pro file, but that would be a last resort. I recommend to stick with qmake to make things simpler for your users until you absolutely need something beefier (unless your build team has a hard-set build environment).
Making major changes to project settings is a great way to mess things up, you'd be surprised. Some settings have effects on certain project configurations that are not always spelled out in the documentation, if at all. Notice that "QtCreator The Application(tm)" does not have the greatest level of detail in its shipped documentation, and glosses over many of its features giving you just the bare minimum detail on some (but not all) items. I have noticed, however that it is slowly getting better. I think we just need more people contributing :3.
Including the top page, the "Qt Creator Documentation" has a rather small number of (13) pages(!) which is hardly enough room to describe every single item within QtCreator. The number 13 is an unlucky number indeed. :3
