Hi Peter,
I've been reviewing changes in glossary output and it seems that MDL-12029 introduced the bug you are seeing. The main thing is that glossary concepts used to be enclosed by <span class="nolink">XXXX</span> and, after fixing that bug, that isn't true anymore.
So, right now, the glossary filter is processing those concepts, instead of allowing the formats to display them properly. So:
1) With glossary filter disabled, it should work ok.
2) Configuring Admin->Modules->Glosary->Formats->Entry List, to display the entries in popup using, say, the dictionary format, should work too.
3) I'll try to re-add the <span class="nolink">XXXX</span> to fix this properly.
1 & 2 are temporal workarounds for the problem until I fix it as commented in 3.
Thanks and ciao 
I think this is intentional, do you remember the details Eloy?