One thing to keep in mind: If there aren’t enough unique inputs, boosting will wreak havoc.
An easy example: my “trivial sequence”: http://mrcslws.com/blocks/2016/03/13/column-overlaps-and-boosting.html
I have 25 unique inputs, 40 active columns, and 2048 columns. That means at most 25 * 40 = 1000 columns will be used. So at any given time, at least 1048 columns are getting starved, and boosting is going to teeter-totter the representations.
I’m not sure if you’re running into this problem, but you might be.