The latter is normal, though. Whether Remote Buddy appears in the 
dock or not is controlled by the NSUIElement property in its 
Info.plist file. Updating through Online Update will add or remove 
this entry according to the previous state of Info.plist, but we run 
into a classic hen-egg-problem with manual updates - Remote Buddy 
would need to run to update its own Info.plist. However, the 
NSUIElement entry is already there at launchtime and can't be changed 
at runtime.

Best regards, 
Felix