IE plug in brings the qlikview code onto the machine and install's it to match IE. however, AJAX is rendered through the browser from the web server. It's presented using a different language than the plug in. We use the AJAX client, it does require a bit of tweaking but it can look exactly the same as the regular client.
Updates in 9.0 might fix a lot of these issues as well.
Thanks for your response Anthony. Question- When you say "tweaking" ; how exactly are your "tweaking" and how do you keep the changes from being overwritten when application is reloaded and distributed?