Permalink Structure

I am currently using the clean permalinks
site.com/final/cookie/ <–LOOKS PRETTY GOOD
But
I have a custom plugin that makes a query on a page.
site.com/final/cookie/?toppingid=23 <—PLUGIN YOUR AWESOME
Whats cool that query does not happen unless you click on a cookie from
site.com/final/<–THE COOKIE IS A WORDPRESS PAGE.YUM SPECIAL TEMPLATE.
The template populates the page page with the data from that query
site.com/final/cookie/?toppingid=23 <—IM BACK!

Heres whats strange…this works in chrome but not firefox or IE… I have a feeling the orginal wordpress permalink format supports the query and the clean url format does not?
IF ANYONE COULD HELP THAT WOULD BE AWESOME
I would have post the link but unfortunately my contract does not allow.