When automating the bypass state of an insert on an Instrument track, the insert bypassed is offset by one in comparison with an Audio track. For example, setting Insert 2 to bypass on an Instrument track seems to bypass the first insert.
This is actually the expected behavior, because the Insert for the Instrument itself is treated as Insert 1 by the track automation. The DSP inserts at the top of the channel strip are numbered from Insert 2 and up.
On Audio tracks, the top DSP insert is considered Insert 1.
