I disagree it's a problem.

going back to Joel again (!) :

"All non-trivial abstractions, to some degree, are leaky."

I talk about this a lot in this particular talk: https://www.youtube.com/watch?v=E09qigk_hnY

Hibernate was a great influence on me but I like to think that it only introduced some ideas in rough form that we've all had many years to improve upon.

The ORM will of course introduce new issues to deal with but this is because it's taking care of a vast amount of persistence code you no longer have to write, and applies a consistency to that persistence logic that would be extremely difficult to achieve without using tools.