Here's something else kinda weird... I changed the mapping in Remote Buddy to execute cursor commands with the virtual keyboard instead of using the Hulu Desktop navigation actions, and it no longer doubled the keystrokes. So it seems to be the combination of slightly inaccurate remote codes and the Hulu navigation actions themselves that causes the issue.

Hope that helps if you decide to try to fix it, but don't worry too much about it because I think the workaround of using the cursor controls will be fine for my needs. It's certainly a better option than trying to retrain the Harmony.