You are converting from your current email server and you have a number of POP3 users. Zimbra by default delivers spam to the Junk folder. You need to override that for your POP3 users. Zimbra by default also ignores user filters on spam delivered to the Junk folder
Solution: Disable the function that prevents filters from working on the Junk folder and create a script to move spam to the Inbox
Allow filters to act on spam
For each COS you use execute the following
zmprov mc MyCOS zimbraSpamApplyUserFilters TRUE
where: MyCOS is the name of the COS
Apply a script to each account that needs this function
zmmailbox -z -m email@example.com addFilterRule "Deliver Spam To Inbox" active any header "X-Spam-Flag" contains "YES" fileinto "Inbox" stop
where: firstname.lastname@example.org is the user that you want to apply this script to.
Repeat for each mailbox as needed.
Removing the script from selected accounts
You may have some accounts you apply this to and you want to remove it later
zmmailbox -z -m email@example.com deleteFilterRule "Deliver Spam To Inbox"
or the user can remove it via the web interface in the under Preferences – Mail – Filters