Couldn't tell you really because I can't stand the idea of separate eybrow parts included as a part of a figure (I'm really glad I bought the original V4 before this "update feature"), but I'll take a stab at it.
I'd say that the eyebrows were moved and inadvertently saved as a part of a face morph, or maybe the default position is up front as a morph target, but when a face morph or expression was saved it was in there too.
When the face expression pose or MT was added, the eyebrows sized up and moved out.
Or maybe it was a full body morph which caused it.
Bear in mind I'm not familiar with this eyebrow thing. Is it a separate mesh? If it's a prop it would react to MT's applied to the figure. If you can find an eybrow MT in the head, set it to an equivalent but negative value. That might work.