Ok I found the issue.
As long as you record outside of a loop, Cubase writes the project tempo into the pool. And if the project has tempo changes, an average tempo will be calculated.
But when recording in a loop, the tempo of the audio in the pool is always “???” resulting in a random tempo at the moment when you switch on “musical mode”, which has completely nothing to do with the actual tempo.
I am gonna open a issue topic with reproduction steps for that.
EDIT: here it is
Tempo in pool not set when recording in a loop - Cubase - Steinberg Forums