Logitech finally updated the Harmony web site with a message, and apparently a fix is available now:

Due to a recent update, an issue has been identified which causes button presses to over respond, sending the same command three times. This affects almost all Harmony users.

If you have updated your remote in the last couple of days, you may be experiencing this issue.

A fix has been released for this issue. Please update your remote to resolve the issue.

We apologize for the inconvenience this may have caused.

Best regards,
The Harmony Support Team