I have also tried the MFCMAPI tool but to no avail.
How did you try using the MFCMAPI tool to fix the issue? Have you tried the following steps with MFCMAPI tool:
1. Launch MFCMAPI tool on the users client.
2. Click Session > Logon, select the Outlook profile and click OK.
3. Double-click Mailbox - your user name
4. Expand Root Container (or Root- Mailbox) > Top of Information Store (or IPM_SUBTREE)
5. Check if you can see the Junk E-mail folder from the list. If so, highlight the Junk E-mail folder in MFCMAPI.
6. Find the PR_ATTR_HIDDEN property from the right panel.
7. Check whether the value is the False. If not, please double click it, uncheck Boolean option and click OK. Now the value should be changed to False.
8. Reopen Outlook to check this issue.
If you have followed above steps and the issue still persists, please try logging into the web mail client of your email account and check if you can see the Junk folder over there.
Please let me know the result.
Regards,
Steve Fan
TechNet Community Support