When registering a MinGW toolchain & qt version manually, Qt Creator will mark the qt version as invalid on next boot.

This is because it cannot run qmake without setting the right environment. BaseQtVersion::queryQMakeVariables has code that tries to re-run qmake in all compatible toolchains then, but the list of toolchains is still empty at this point:

QtVersionManager::updateFromInstaller is called in QtSupportPlugin::extensionsInitialized(),

while

ToolchainManager::restoreToolchains is called in ProjectExplorer::extensionsInitialized()