Is that using the subst_ command or just regular objects?

Do you accidentally ahve some groups in there which do not begin with gp_? I think this is probably a problem with naming the objects and the number of underscores.

As a reminder:

All groups must begin with gp_ (single underscore)
Ignored objects: ignore_ (single underscore)
Substituted entities: subst_ (single underscore)

Maya geometry entities go

Cube0__skill1__skill2 etc etc (double underscores)
Cube1__1234__123432__12341

__n1234 = 1234
__n123_5 = -123.5

In skills, a single underscore represents a decimal and n makes it negative