Custom shortcut interferes with system shortcut in save dialog on Mac OS X

I have assigned custom shortcuts to the swap_line_up/down commands. The shortcuts are alt+up_arrow and alt+down_arrow. These shortcuts are also used by Mac OS X to navigate to the beginning, respectively to the end of a list of files in Finder or in Open or Save dialogs.

The problem appears when I try to "Save As..." a file or project and in the opened dialog I try to use the system's shortcut. Sublime seems to intercept the keystrokes and doesn't let them bubble to the OS although the editor doesn't have the focus anymore.