Hi, colinrobot,
Unfortunately, I don't have a solution, but I'm experiencing something very similar, so I wonder if the issues are related. I am also experiencing pattern "bleed" when playing patterns in a chain. Here are my steps to reproduce using the Drum sequencer (pattern numbers are arbitrary--I just so happened to be using these numbers the latest time the issue occured):
1. BSP upgraded to v2.0.0.2 firmware
2. Create 4 measure pattern on Drum 2
*NOTE: I sequenced no steps on the bottom right pad (C 1/32)
3. Create different 4 measure pattern on Drum 3
*NOTE: for pattern 3, I DID sequence every step on the bottom right pad (C 1/32)
4. Create a Scene that chains 2 and 3 together
5. Play the Scene
Expected Result
Pattern 2 plays normally, followed by Pattern 3 playing normally, repeat endlessly/happily
Actual Result
Pattern 2 plays normally, followed by Pattern 3 playing normally, but when Pattern 2 plays again, the last 3 measures of Pattern 2 are permanently replaced by the last 3 (or maybe just last 1) measure of Pattern 3. The Scene continues alternating between 2 and 3, as expected, but Pattern 2 is forever altered.
I haven't found any solutions to this; again, it seems to be the same (or at least incredibly similar) issue colinrobot is experiencing.