I couldn't reproduce your issue using the same combination of software. Coverflow actions are working perfectly here.

Using custom keystrokes most certainly won't work, because all that'd do is toggle CoverFlow mode on/off in iTunes. It wouldn't solve the problem that you'll also need to send keystrokes to navigate in that mode. The built-in CoverFlow support solves all of these.

On a general note, please be aware that, if you use the default settings of newly created keystroke actors, the press and release of all keystroke actors happens at the same time, so you'd get CMD + F + ALT + 5. If you want to subsequently execute a number of keystrokes, you'll want to change the settings of the keystroke to only execute once when the button is pressed.

Regarding your issue, I believe it to be rooted in an unfortunate combination of changes to Remote Buddy's default configuration. Please file a support inquiry via http://www.iospirit.com/contact/ if you'd like one-to-one support in finding and fixing the issue.

Best regards, 
Felix Schwarz