I assume from your description that your application launches multiple processes and that you've left "Profile child processes" ticked. Does the initial process shutdown after you've logged in?
What version of .net are you compiled against? if you can compile against .net 4 then you should be able to use the "attach to .net 4 process" option to capture the information you require.
If you're still having trouble, you can get in touch with support @ red-gate . com with F0039339 in the subject line for more in depth investigation.