I couldn't re-produce this with a minimal example, so here it is with qtcreator.pro:

1. Set a breakpoint in the last line of QmakeProject::updateCppCodeModel() in current 3.6 qtcreator.pro sources.
2. "Start Debugging"
3. Create a "Qt Console Application" from the wizard.
4. The debugger will stop on the breakpoint, expand pinfo, expand m_projectParts, expand [0], expand data - compare the display of the value toolchainDefines and projectDefines in the attached screenshot. Both contain newlines but are displayed differently.