I just tried, and could not reproduce an issue.
- Start a new project from the BLANK template using File > New.
- Verify clock is defaulted to 'Internal', and Metronome is set to use a MIDI note.
- Insert a MIDI track and arm it.
- Record MIDI from a keyboard synth.
- Play back the MIDI driving the direct-monitored keyboard synth.
- Save, Close, Re-open, and Start/Stop playback again.
After doing all that, I verified the clock was still set to 'Internal'.