Applications are identified by Remote Buddy using their bundle 
identifier. I don't see any change regarding this with VLC - neither 
in the release version nor in the nightly builds version. But for the 
sake of completeness: did you download your copy of VLC from the 
official VLC website? Or are you using a copy provided by another 
source?

To see whether an app is installed or not, Remote Buddy asks OS X 
Launch Services - which keeps records on the location and file types 
of all applications - for information on the respective application.

If an application is not found this way at the time Remote Buddy is 
starting, the respective Behaviour is not used by Remote Buddy.

Have you started VLC at least once after updating to VLC 0.9.9a, but 
before starting Remote Buddy?

I ask, because VLC may still be in OS X download quarantine and thus 
be treated as non-existant by the OS X Launch Services. VLC (or any 
other downloaded software) will not turn up in Launch Services' 
database before it wasn't started at least once.

Best regards, 
Felix Schwarz