This happened to me too. Mailed support about it, but no solution.
From what I experienced, this issue was related to setting different lengths for different tracks. Whenever I got this message, I had to load a different project for the message to disappear. When I loaded the project that I got the message with again, all tracks were set back to their default length of 16 steps.
So, after this I haven’t use different lengths in patterns anymore, and since then I didn’t get that message. Weird stuff, I hope it will be fixed.