This posting is older than 6 months and can contain outdated information.
A refresh bug has been fixed in the settings, but I don't see how that 
could remove any changes as it strictly deals with display code rather 
than data modification. Other than that, no changes were made in the 
configuration interface between 1.7 and 1.7.4. Also no identifiers - 
which configuration heavily relies on - have been changed ever since 
the first release preview of Remote Buddy back 1 1/2 years ago.
Remote Buddy keeps all of its settings in plists located at ~/Library/ 
Preferences/com.iospirit.remotebuddy.*.plist.
These plists are written in an especially safe manner: OS X first 
creates a new, temporary file. And only after it succeeded saving that 
file will it replace the old with the new copy.
This way, even if the app crashes while preferences are saved, the 
file's content still remains intact. This method of saving files is 
also called "atomic".
The only occasion where I ever experienced this strategy being turned 
into the opposite, effectively replacing all updates prefs files with 
zero length files, was when I recorded something in EyeTV and the HDD 
would get filled up to its last byte. Apple Mail would then usually 
greet me with its "Welcome to Mail - do you want to configure a mail 
account?" screen when I started it next time.
This kind of scenario (a full system partition and OS X choking on it) 
is the only way I could see the loss of any Remote Buddy settings 
happening.
Maybe the problem lies elsewhere, but then I'll need more info from 
you - Behaviours and profiles are two very different things and I 
don't see how the choice of one would logically affect the other.
Best regards, 
Felix