The following link might be helpful: Thunderbird and Junk / Spam Messages https://support.mozilla.org/en-US/kb/thunderbird-and-junk-spam-messages

Quotations from the above link:

To guarantee that important messages will NOT be marked as junk, use Whitelisting.

Whitelisting Under Do not automatically mark mail as junk if the sender is in you can select address books which will be used as a whitelist. Senders whose email address is in a whitelisted address book are exempt and will not be automatically marked as junk by Thunderbird. But you can still manually marking a message containing a whitelisted address as junk. It is recommended that you enable whitelisting to help ensure that messages from people you most care about will not be marked as junk.

Tell Thunderbird what is NOT Junk Sometimes Thunderbird's junk filter might get it wrong and mark good messages as junk. Therefore, it is just as important to tell the filter which messages are not junk, especially on a new installation of Thunderbird. Note: You should frequently (daily or weekly) check your Junk folder for good messages wrongly marked as Junk by Thunderbird and mark them as Not Junk. This will recover the good messages and improve the correctness of the filter for the future.

Try whitelisting the senders with the spam/junk controls available in webmail settings and avoid the TB junk controls.

Whitelisting does not work for me, emails I have whitelisted are still filtered as spam by Thunderbird. Using the "mark as not spam" also does not work. I have even tried turning off the spam filter, logging out of Thunderbird and back in and emails are still be marked as spam.

If you have whitelisted then you need to examine the messages in the spam folder. Do they have the orange/red flame icon?