Here's our problem in a nutshell...
A plugin we built for rating comments works perfectly without permalinks active. Part of this plugin places a rater in the "loop" of each comment. Its just a small html form. Everything, including checking for login, rating, tracking the ratings all works perfectly until that is we activate permalinks. Then the rater simply disappears. The source code of the resulting page shows nothing but the div that holds the rater. The function call doenst run.
My guess is that it has something to do with htaccess and the way the comment ID (which is how we are accessing the comments to rate them) is rewritten.
Has anyone experienced any problems with permalinks breaking plugins and found any solutions?
We're building on staging server so I dont have a live example i can post but can supply lots more information if you can tell me what you need to help us sort this out.