They should be separate in the local store unless something is corrupt. Are
they shared online too? If not then it's just Outlook acting goofy and I'd
start with deleting the *.ost (or *.msnpst if you've used the connector
since last fall). They are just local caches, so you won't lose and data, as
long as it has synced.

Outlook stores your messages stores (OST and PST) as hidden files in
C:\Documents and Settings\username\Local Settings\Application
Data\Microsoft\Outlook. You can easily access it by pasting
%USERPROFILE%\Local Settings\Application Data\Microsoft\Outlook
in the Address bar of your browser or Windows Explorer.