Are you using mapped keys in ISBoxer to trigger the GS macros? ISboxer triggers it's own macros without issue, so there should be no reason why there are any issues triggering other non ISBoxer macros, and it does as it can trigger most peoples "roll yer own" macros.

So, leaves an interesting dilemma, in that there is something odd in the configuration of your macro, or there is something odd in your configuration of ISBoxer. The latter only really applies if you are trying to trigger your macro from an ISBoxer mapped key, or you happen to have double bound a hotkey for your in game macro to something that ISBoxer is sending for some other purpose.

In either case, it would be helpful to see your ISBoxer profile, and a macro definition or two.

http://www.isboxer.com/wiki/Configuration_Sharing