I have run into this a couple of times when going back and forth between linux and windows. For example, before opening the project on linux (after it has been build on windows), I do the following:
1) delete Debug and Release folders
2) delete Makefile, Makefile.Debug and Makefile.Release
3) delete object_script.* files
4) delete <project>.pro.user file

then open the project in Qt Creator and rebuild.

When going from linux to windows the steps are similar although some of the intermediate files are called slightly different.

hope this helps.