Two problems when rendering:
1: the song contains tempo changes. I render an entire track that contains an AU-synth that uses an arpeggiator. These tempo changes are not there in the rendered file. The arpeggiator in the audio file plays back at the tempo of the first bar. When playing back the original track (so no rendering took place), the arpeggiator follows the tempo correctly.
2: When I render part of a track (with an AU-synth that uses an arp), the midi notes of that part of the original track are gone.