Sorry I wanted to add to the other post, but it won't let me reply.
So all my domains are set to dedicated app pools, this works fine and they are created properly.
However, when clicking the green button to enable APE, the site is then moved out of its dedicated app pool and just put in the "ASP.NET 4.0 (Integrated) one instead of just switching to the its own integrated one.
I should have fixed the issue where you can't answer your own post (was an issue that slipped in updating the site).
Regarding helicon ape it's an odd issue.
I will add it to the bug tracker but i am not sure if this can be fixed before the jan version.
Thanks Marco.
For anyone else reading, the workaround is of course to default the ASP.NET application pools to be the "Integrated" type and not "Classic"
