Last time I looked into this, I found that Profiler was setting up its' own hard-coded application pool configuration. Naturally, it has to make a few changes so it will run outside or IIS, but it always sets up the application pool in "classic" mode, which causes some problems.
I'd try out the ANTS Application Host, which will run your web application as a console app that you can profile. This program will copy your app pool configuration and overwrite the bits that it needs to in order to allow profiling to work. Here is a link to it:
ftp://support.red-gate.com/patches/ants ... Host11.zip