I just upgraded from X3e to Platinum too - and use Audition too.
I found that I couldn't run Audition from the tools menu - because SONAR is 'run as administrator' and Audition wasn't. When I run Audition as administrator (set in them shortcut) - it works from the tools menu!
I never tried it standalone at that point - but everything works now by running both as administrator (Audition definitely runs standalone this way).
I don't know why it should matter - but is it OK for you to just run both as administrator? If so, you should be OK. If not - did you try setting SONAR to not 'run as administrator'? And see if that works?