ISBoxer isn't using shift for anything that should be affecting your macro, no. (unless you've checked "Use FTL Modifiers" for some reason) But without seeing your config, I really don't know what you're doing with the macro or the key combination to say why it wouldn't work.

I will explain how it's intended to work in ISBoxer 38, though. Instead of using WoW Macro Actions, you put this macro in the WoW Macro library under Game Helpers (recommended for anyone setting up new macros), and you check the optional modifier box(es) that match your [mod] tags. In this case, left shift would do. Then you assign it a Key Combination that does not include any of the optional modifiers.

To use this macro in a Mapped Key, set up a Named WoW Macro Action. The optional modifier boxes checked in the WoW Macro will be available as options on the WoW Macro, and ISBoxer will combine any of the optional checked modifiers with the Key Combination assigned to the WoW Macro when it is supposed to send this keystroke.

None of this should have "Use FTL Modifiers" enabled, and also doesn't need Hold enabled.