This posting is older than 6 months and can contain outdated information.
Please allow me to just quote the FAQ entry I added a few hours ago 
regarding this:
-- cut --
After an update, Remote Buddy appears both in the menu and the dock 
although I've chosen another setting. (FAQ015E0208)
Whether or not an application appears in the dock is determined by an 
attribute in the Info.plist contained in the application's bundle. The 
value of this attribute determines whether or not an applications 
appears in the dock over its entire run time. It is not possible for 
an application to change this attribute at run time. 
If you install Remote Buddy manually or if the Online Updater does not 
have sufficient rights to adjust this file, Remote Buddy will appear 
in the dock regardless of which setting you choose.
In order to change the settings, please proceed as detailed below:
• Please make sure Remote Buddy has the sufficient rights to change 
the Info.plist contained in its application (app) bundle. 
• Open Remote Buddy's preferences. 
• Choose a different setting for the option "Remote Buddy appears" 
• Choose the setting you want for the option "Remote Buddy appears" 
• Restart Remote Buddy.