Please note that the AU MIDI plug-in option comes with Rec To Track and MIDI Thru buttons in the effect rack, which allows you to determine the recording behavior.
I have a similar problem in Cubasis 3. I want to record the Midi output of an AU appergiator to a new midi track for detailed editing.
In “Routing” I set the midi output of the track 1 with the appergiator midi effect to an empty midi track 2 (Now automatically the input of this empty track 2 is set to the track 1 with midi effect).
After recording the part, I have the wished appergios in track 2 as midi BUT (here comes the problem) it also directly records the original midi notes I played on track 1 (the longer notes that are routed into the appergiator to achieve the appergios).
How can I get JUST the appergios, without manually removing the original notes?