Sorry if this obvious but I missed it.
In moodle 1+ as I last remembered this, words in the glossary had a light grey box around them. Now in Moodle 2 they look just like all other URLs in colour etc. I know the cursor is a question mark instead of pointing finger but IMHO the effect on a learner reading a paragraph with numerous glossary words in it (it happens) and one link you want them definitely use, they have a tendancy to ignore the "real" URL . Haven't done robust research but I'll bet on it .
This doesn't look like a theme issue and is there any way to change them back to the grey boxes ... easily in terms for coding dummies please