We have been running Version 11 SR2 and recently upgraded to SR5 to resolve some bugs. In our environment we do not let the end user see the AccessPointat all. Instead we present a web based portal of our own making which displays only the links to reports that they are allowed to view. Much like you say above, its a long URL but by doing this we force what report they open and the use of IEPlugin.
This means that the user would open our web page, click on a report link and have that report open in another browser tab without any evidence of AccessPoint.
Since going to SR5 they are now taken to AccessPoint on the first click. but if they close the AccessPoint browser window and click on our report link again, the proper report opens up.
We have updated to the latest IEPlugin but still have no luck. Everything works fine with AJAX but we prefer IEPlugin as it renders the reports much nicer and seems to handle large listboxes better.