Are you putting BE.net in the root folder of your website or is it in a subdirectory?
I've got a couple of installs where BE.Net resides in subfolder (/blog/ or /customergalleries/) of the root where the store lives and have had no problem. I did need to add a few lines to the web.config for the blog as shown below but it seems to work fine.
BTW - The blog resides in a virtual directory under the store, not in a physical directory. That way I can upgrade one or the other separately.
<!-- MJGMod: Added to make this work underneath ASPDNSF -->
<remove verb="*" path="action.axd" />
<remove verb="*" path="execpackage.aspx" />
<remove verb="*" path="googlemall.aspx" />
<!-- End MJGMod -->
Best of luck to you!