When I call a bootboox alert or confirm in my body appear a "style="padding-right: 15px;" automatically and this not disappear after a I close the bootbox alert/confirm.
Sorry for bad english, but basically bootbox give for a body element one padding-right(with 15px) nonexistent in my css.
This is actually being added by the Bootstrap modal plugin itself, to account for the overlay temporarily "hiding" the scrollbar. What version of Bootstrap are you using? I think this was a monkey patch that's since been removed, if I recall correctly.
So I'm using Bootstrap 3.3.7 and Bootbox 4.4.0.