All I can figure is that you are using POP3 accounts and you used to have both of them using the same PST file. But when you did the most recent setup you didn't tell Outlook that secondary.com should use the same PST file as primary.com.

If this is the case, you should be able to either "Change Folder" for secondary.com or remove and re-add it and tell Outlook to use "Existing Outlook Data File" as described in

Deliver All POP3 Accounts to One Outlook Inbox | Slipstick Systems

And the "Change the PST file after adding the account" and "Add the Account using Mail Setup dialog" sections of
Manually add POP or IMAP accounts to Outlook | Slipstick Systems