I'm getting them when changing Scenes or Channels from Axe-Edit and from the front panel, with the editor paused. The channel switching is really fast though.This has been fixed for the next release. Gapless changes weren't working correctly when using an FC or a switch due to a task priority issue.
Here is a quick preset with a Synth block, a Flanger, a Delay, and an Output 1 block. Try going between various scene combinations.