I’ve downloaded and tested Remote Buddy with the latest pre-1.0 Plex/HT build not long ago, and everything worked without any problems. So that this would change with an incremental update comes as a surprise.

I’ll look into this and get in touch with Plex Inc if necessary. Meanwhile, please keep in mind that Plex is highly complex under the hood and the sources for problems can be manifold - and in the past most problems I’m aware of were actually caused by old or customized config Plex files/helper tools.

Until I’ve had a chance to look into this, you should be able to use the Virtual Remote to send emulated Apple Remote button presses to Plex’ own PlexHelper (which should work, unless a PlexHelper of a previous Plex version keeps the PlexHTHelper from using the Apple Remote - as has been reported to me many times with Plex/HT pre-1.0. In that case, you can use Remote Control Diagnostics to locate and remove the old Plex’ version helper).

The steps for using the Virtual Remote are identical to what can be found here under "I'd like to use the Harmony remote mode of Plex“: 
http://www.iospirit.com/blog/article/131/Remote-Buddy-and-Boxee-Plex-and-XBMC/

Best regards, 
Felix Schwarz