The young singer's difficulty with theory class and the Chopin Preludes are not unrelated. I was first assigned the Preludes as a teenager. I recall bafflement: what was the relationship between No. 2 and the key of A minor, or No. 4 and E minor? Already a kind of theoretical rigor mortis seemed to have set in.
Played sequentially the Preludes make clear that Chopin hears tonality on the piano as a function of the variability of fundamentals and overtones: why can't a tonic tone by present as an overtone before it is explicitly a fundamental? Overtone interaction is much more in evidence if the pieces are played sequentially than if played out of context.
Confusing overtones with fundamentals is the most common problem I have encountered with people having trouble adjusting to theory and ear-training. That finding is corroborated by people who run ear-training programs. I deal with the phenomenon as it affects either individuals wanting to feel good about playing the piano or people singing or playing in small groups.