I was getting strange index letters when moving to Unicode in Czech; what helped in my case was modifying the following line in mod/glossary/view.php (approx. line no. 340):
original line: $pivot = $pivot;
modified line: $pivot = mb_substr($pivot, 0, 1, get_string("thischarset","moodle"));
You may try experimenting with the fourth parameter (encoding) in mb_substr, if the proposed solution doesn't work right away.
Hope this helps.