Tempo changes persist until the next change is encountered. If the initial tempo at 1:01:000 is not persisting, there must be another tempo change later on. Check Views > Tempo to find and delete that change.
But I'm not sure what you mean about the project tempo not following the "tempo" of your interface. The interface just provides a clock signal that gives SONAR an absolute time reference; the interface doesn't know anything about musical tempo.
If the metronome is out of sync with the audio, that just means the M:B:T timeline isn't aligned with the audio. That will happen if you change the project tempo after recording audio to a click at another tempo. You would have to enable autostretch on the clip for it to follow the tempo change.