I am seeing the same effect in my test implementation as well. The problem is that multiple active cells per column is very similar to bursting, and has a similar effect to what Vovchik described for certain input sequence, where subsequent cells wind up being encoded in multiple sequences (thus accumulating multiple predictions, which in turn can result in multiple active cells in the next columns for certain input sequences, and so-on). The system almost needs to look back more than one time step when it is adjusting connections, so that it can recognize when one cell winds up being part of two similar sequences, so it can correct the issue. Before I go that route, though, think I will play around with NuPIC to see how it handles these scenarios, or if it has the same behavior.