This is now fixed for me in the latest Moodle 2.6.1+ (Build: 20140213)
Glossary popup now centred in the page
However, have noticed a couple of other issues:
1. If more than one glossary item is selected, without closing any popup using the [OK] button, resulting in multiple overlying popups, it is only possible to close the uppermost popup using the [OK] button. The remaining popups can only be cleared by a browser page refresh. Not a huge issue, but still not very elegant.
2. There is also a problem with auto-linked Glossaries in pages that use the Jmol (3D chemistry structure) filter. When a glossary entry is selected, multiple popups appear each having "alert" as the title, and the text as "confirm". Changing the relative orders that the filters are applied does not change this behaviour. See also: https://github.com/geoffrowland/moodle-filter_jmol/issues/9
$link = new moodle_url('/mod/glossary/showentry.php', array( 'courseid'=>$courseid, 'eid'=>$concept->id, 'displayformat'=>'dictionary' ));
$link = new moodle_url('/mod/glossary/showentry.php', array( 'courseid'=>$courseid, 'concept'=>$concept->concept, 'displayformat'=>'dictionary' ));
However, I'm not very familiar with the Glossary code and I don't fully understand this apparent fix, or possible knock-on effects, though it may give further clues to the underlying cause.
Appreciate that this may be as much a Jmol issue as a Glossary issue. However, since Jmol is 3rd-party code, it may be easier to fix from the Glossary 'end-of-things'.
Any insight or suggestions gratefully received!