I cannot reproduce the problem - either on 1.9 or 2.0. The examples you give display OK.
Do those expressions appear in the glossary concept field or definition (the latter, I presume).
Moodle 1.9 or 2.0?
Greek characters not displayed when viewing the glossary itself or in the glossary popup window which appears when clicking on the glossary autolinks in a text on your site?
Please provide as many details as possible, including screenshots, export your "problem glossary" (or part of it) and attach it to a further post here so I can examine it.
Joseph