Sven,

You also have to take into account that you have reflections from the
glass surfaces (front and back) that will change your resist profile
compared to say silicon substrates. So it's not surprising that your
openings are larger at the glass surface.

Also, the roughness of glass means that photoresist will adhere much more
strongly than polished silicon (due to a larger surface area contact) so
you might want to shorten your bake times and/or go to lower temperatures.
If you're using adhesion promoters, you might try going without them.

Mike