I noticed something similar with the newest firmware. It was updated to prevent others that were getting a lot of phantom or repeat keypresses. Now I don't get repeats when I hold the button, but if I manually repeat the keypresses it works pretty well. previously I had some repeat keypresses so the new firmware seems more predictable, but I'm having the same issue you are.
If Jason makes a new beta firmware to address this, I'll test with my Harmony on the Roku profile.