Please clarify: you're stating that Thunderbird has junkmail, but not spam, and the server has spam, but not junkmail. true? If a message is moved to junkmail, does it show up in spam folder?

I have since switched the account over to POP3 so spam isn't showing up in both, only locally.

re :I have since switched the account over to POP3

You cannot simply alter the server settings of an imap account and insert the pop server settings. You must remove the imap account account first and then create the Pop account.

Did you remove the the Imap account and then create a new Pop account? If yes, then you will not see any folder that is on the server - as seen via webmail. Pop accounts will have their own set of default folders created by Thunderbird. Pop accounts can only access the server Inbox and download whatever is in it. Any emails the server puts into the server 'Spam' folder will never be downloaded to Thunderbird.

re :I have 2 accounts in TB. In one of them Thunderbird has a folder named 'Junkmail' but on the server the folder is called 'Spam.' Thunderbird is not allowing me to rename the folder.

That can occur if there is both a 'Spam' and a 'junkmail' folder on the server. Sometimes a 'junkmail' folder can be a residual folder from eg: a verizon account which got moved to another server where there is 'Spam' folder. You would be able to 'subscribe' to see any folder on the server. You would not be able to 'rename' something that is set up as the default junk/spam folder. That default folder would need to have the flag for Junk' removed so it appears asa normal folder in order to rename - however, you should do that when there is already a default 'Spam' folder which the server uses. You should 'unsubscribe' from seeing the 'junkmail' and make sure you are subscribed to see the 'Spam' folder. Then make sure the Account Settings > Junk Settings' are set up to use 'Other' and select 'Spam folder on mail account name'.

I was making a long story short. I did remove the account first then added it as a pop3.