glossary auto-linking speed is affected by some different variables:
- Number of items in your glossaries.
- Speed of your server.
- Caching time.
The time necessary to auto-link your tests is directly proportional to the number of items in your glossaries. Perhaps you should reduce the number of items to be linked (deactivating their "auto-link" variable).
Obviously, the speed of your server is a crucial variable. Differences can be notable!!
And finally, increasing caching time for filters can help to improve things, but the 1st time or when the cache is expired you will notice the slow-down.
As Moodle is evolving every day, I'm sure we'll see some improvements in this area soon (I'm thinking about some possibilities just now).