I was having these issues as well, and I thought I'd post my solution.
I'm using the Samsung LN46C650L1F manufacturer, and I have 0ms for my inter-key delay in the Harmony Remote Software. I am also using an IR repeater, which probably exasperated my problem.
Even after using these tweaks that this community recommended, I was still having major issues with keys getting "stuck". I would press the down arrow twice, and it would scroll sometimes for 5-10 seconds. The final fix was to change a deep menu in the software, which I got from the user nooz over at the XBMC forums on this post.
I hope this helps someone else, since I've spent a number of hours tweaking this like crazy!
