This should be my IS Boxer profile http://pastebin.com/KV6Pt39e (never used pastebin before so I'm hoping this is done right)
This is an Elemental Shaman GS macro i use http://pastebin.com/wW36GWxS

Prior to using GS is just had a standard Key Map - Combat set of keys using F6-F12 which sends an assist and the key hit to each warcraft window.
I had F6 to F12 bound to an action bar in game and just cycle pressed those keys which contained either an in game macro or a spell.

The GS macro I use is really just a condensed version of what I had in the action bar.
For Eg
F6 = /castsequence reset=target/15 Flame Shock,a
F7 = Lava Burst
F8 = /castsequence reset=combat Lightning Bolt,Lightning Bolt,Lightning Bolt,Lightning Bolt,Earth Shock,Lightning Bolt,Lightning Bolt,Lightning Bolt,Earth Shock,Lightning Bolt,Flame Shock

So combining GS and IS Boxer I wanted to just spam F6 and have it cycle the GS macro on all windows.
As another angle of trouble shooting I tried this using Keyclone and it worked across all windows.
I also tries using a different Mapped Key in IS boxer to see if the key I was using was the issue but even with a different key the issue remained.

So it's probably something to do with my IS setup I'm going to guess.