Remote Buddy never had direct support for shell scripting-

The only way to execute .command files directly via Remote Buddy is either

a) via Remote Buddy's file browser 
b) when you added such a file to the menu via drag & drop from the Finder

In both cases, Remote Buddy will ask Launch Services for the applications capable of handling this file type and

a) either open it directly with it (if only one application is capable of handling it) 
b) offer you the choice to choose an application to open the file, preselecting the default one for you

In the case of .command files, the default application is Terminal.app. Please check in Finder whether Terminal.app is still the default application for .command files and adjust it as necessary. You can do this by right clicking on a .command file in Finder and then select "Get Info" from the popup. There you'll find both the default application info as well as the ability to change it.

To execute a script from within a custom action in Remote Buddy, you can use AppleScript. Apple has a nice TechNote on this: 
http://developer.apple.com/mac/library/technotes/tn2002/tn2065.html

Best regards, 
Felix Schwarz