This posting is older than 6 months and can contain outdated information.
The MythTV developers (or those providing new builds on their own) 
seem to have a passion for frequently changing their bundle identifier 
it appears.
Since Remote Buddy (and OS X, CFPreferences, etc., etc.) identifies 
applications not by their name, but by their bundle identifier, if 
MythTV's bundle identifier changes from
org.mythtv.macx.mythfrontend
(currently used) to f.ex.
org.mythtv.mac.os.x.mythfrontend
Remote Buddy has no chance to see its the same software. Also, 
checking for the existance of the app on startup will of course fail, 
if you removed the old copy (with org.mythtv.macx.mythfrontend, as in 
the Behaviour) and replaced it with a new copy of MythTV (using 
something else than org.mythtv.macx.mythfrontend).
Your settings of course still exist. It's just simple impossible for 
RB to detect the latest mindchange by the MythTV developers/"builders".
The quick solution for you is to simple change the value of 
CFBundleIdentifier in the Info.plist to org.mythtv.macx.mythfrontend .
The real solution is to get the MythTV developers/"builders" use the 
same bundle identifier in their Info.plist just like everybody else is 
doing and stop using different bundle identifiers.
Where did you download your copy of MythTV?
Best regards, 
Felix Schwarz