Is the second account a unique account, in it's own mailbox on the server?
If you have a catchall account and use the same username and password to download the mail for both addresses, it's a catchall - outlook doesn't sort by email address, it downloads everything in the mailbox. You can use rules to move the mail the other folder.
If the above doesn't apply, are their rules moving the mail? did you try selecting a different folder in Change Folder, applying it, then reselecting the correct folder?