Hi -
Yes, that's often the case. MIDI tracks are just data -- they trigger the same audio samples/sounds regardless of the Tempo, so they can easily be sped up or slowed down as much as desired and the audio will sound fine. But Audio tracks are fixed at the Tempo they were originally recorded at -- when their Tempo is changed [by enabling Flex on the Audio tracks] GB has to do a lot of complex under-the-hood processing to change the speed while preserving the pitch -- depending on the specific material, this can sometimes cause artifacts [like the warbling you described]. Usually GB should sound ok with Tempo changes of a few BPM, but larger changes in Tempo (10-20) BPM may occasionally result in artifacts.
