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After reading the Launch Services Reference at:
http://developer.apple.com/mac/library/documentation/Carbon/Reference/LaunchServicesReference/Reference/reference.html
... Finder itself uses Launch Services to open applications, documents, and URLs ...
Reading this makes it seem to me that if the Finder is able to utilise Launch Services to pass the .command files to the terminal that there is an issue with the way Remote buddy is interacting with the Launch Services API.
Also the open command which utilises Launch Services is correctly launching .command files.
Are you using LSGetApplicationForItem to generate the list of applications displayed in the Remote buddy file manager?
I will endeavour to try and determine if this is indeed an issue with the Launch Services API, my install of OS X or if in fact there a bug in Remote Buddy.
Can you please confirm that Remote Buddy is still able to launch files with the .command extension and so I know that this issue is confined to just my case.
Could you also tell me the version of OS X you are using where this works so that I can try and reproduce your success.
Thanks for your time,
Sefton