try starting process Explorer (part of SysInternals tool set by Mark Russinovich) before starting Notes.
collapse the winnt.exe part of the process tree to focus on user processes. Start Notes, and observe what is started with Notes. Now you can see what is active when the stall occurs. For me it was a problem with ndyncfg.exe even though DisableDynConfigClient=1 is in the Notes.ini
If it's one of the general Notes processes, Process Explorer also let's you check which threads are responsible for CPU usage.