When you record audio in cycle mode in Logic Pro or Logic Express, Logic mutes all previous takes and creates new tracks for each cycle iteration—even when the "Auto mute in cycle record" and "Auto create tracks in cycle record" options are not enabled.
These two settings only apply to MIDI regions, which can be stacked on a track so that all takes play together (as long as the receiving module or Audio Instrument has sufficient polyphony to play all the notes).
Audio regions can't be stacked in the same way, since only one audio region can play at any given point on an audio channel. Because of this, Logic always creates new tracks when recording audio in cycle mode, and mutes regions created from previous iterations to ensure that the current recording is always audible. You may then selectively unmute regions from previous cycle iterations.