The balancing properties of a gömböc are affected by mechanical defects and dust both on its body and on the surface on which it rests. If damaged, the process of restoring the original shape is more complex than producing a new one.
Dropping an eyelash on it, and using a standard kitchen table probably won't make it fail, and it will probably still work -- but it does impact it at the theoretical absolute level.
Close to the stable and unstable equilibrium points, any imperfections create additional equilibrium points, like someone else mentioned.
The threshold will grow with the distance to equilibrium points, so in some places, an eye lash, a grain of sand or the inscribed logo makes absolutely no difference.
For an interesting analysis of a practical application of this, namely turtles and tortoises righting themselves, there's a full text analysis of the dynamics involved available here: http://rspb.royalsocietypublishing.org/content/275/1630/11.f...
Here's the actual clip on Youtube http://www.youtube.com/watch?v=XCAg5_vHFmI
(And that's leaving aside the more fundamental point that the very definition of a Gömböc isn't applicable in the physical world, where objects do not have precisely defined edges and cannot be completely homogenous).