I think the geogebra display problem is fixed now on https://demo.webwork.rochester.edu/webwork2/2017_UR_WW_workshop/geogebra/
The problem appears to be a change in the geogebra code imported to run the geogebra applet. In order to accommodate the change by the geogebra site we've modified code in Applet.pm. This was done in pull requests:
https://github.com/openwebwork/pg/pull/354
and 355.
They have been incorporated into the master branch and the develop branch respectively so updating your code base using github will restore the proper display of geogebra applets.
You can also view the changes (only a few lines) by following the link above.
WeBWorK Main Forum
Overlapping Text with entry cells when using GeoGebra
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