Multiple text indicators appearing

Drupal 5
Glossary 5.x-2.6
TinyMCE
(let me know if you need more details about config)

I've always had an issue where the glossary module was breaking in-content links when the text editor was used. I was working around this by using the php code setting and flipping back and forth between the text editor as needed to enter content. This was a huge inconvenience for the client... just one more thing to remember when entering content. Seems to be similar to http://drupal.org/node/315842

Recently, and I haven't changed anything, we've been getting multiple indicators added to terms. It seems like the filter isn't removing the old indicators and tagging the term again. In some cases 4 indicators are added.

This is great functionality to provide via a module, but I haven't been able to get it working issue free. I'm getting to the point where I have to tell the client we're going to have to disable this feature. Any ideas? Any one with similar issues I'd love to compare notes to see if a smoking gun can be found.