I'm not sure if you can send modifiers with a mouse button on a keymap.
I know you can with a repeater region.

I do macro's with mods in them do work in ISBoxer.
I have a Keymap which sends 1 (output) to all windows when I press 1 (hotkey).
And another Keymap which sends Alt 1 (output) to all windows when I press Alt 1 (hotkey).
One of my shammies has dual spec, and only adds DPS when I press 1 + Alt.

However until making the second keymap, Alt + 1 did not activate my Keymap.
So nothing happened on any toon at that point.
But two keymaps, one with the mod and one without, on key 1 works great.