This is a problem reported by another user in the forum. i have the same problem with 2.0.3 and he doesn't know how to report, so i did:
quote:
[...]
Sometimes the glossary-entry opens in a java-script-window (yui-window), and sometimes the entry open in a link.
A solutions:
In administration /Plugins /Filters /Common filter settings edit the field "Text cache lifetime" Choose "No"
Now your Server filter every page and does not use the text-cache. The page will always open in a java-script-window.
The disadvantage: The server needs more time to produce the page.
Background:
Whenever Moodle use the text from the text cache, it does not insert in the header the following line:
Y.use("moodle-mod_glossary-autolinker",function() {M.mod_glossary.init_filter_autolinking(

);})
Result: the javascript-window does not work.
Without this line the Links do not open in inline-windows.
[...]
source http://moodle.org/mod/forum/discuss.php?d=174486&parent=780062

Replication instructions:

• create new global glossary and create a new word
• enable filter & auto-linking somewhere. e.g. in a course
• enter this course
• the word is highlighted as a glossary item but when you click on it, you'll be redirected to the page of that item (mod/glossary/showentry.php?courseid=1&eid=2&displayformat=dictionary e.g.) instead of a popup window
• this does not happen if you check /Plugins /Filters /Common filter settings edit the field "Text cache lifetime" and choose "No"