Typically, server-based mailboxes should appear the top of the list of mailboxes in M2FMI. However, if you have not done so already, please be sure to scroll through the complete list of mailboxes in M2FMI, in case the mailbox in question resides at the bottom of the list.
If the mailbox still does not show up in M2FMI's list of mailboxes, then it may be inaccessible. In this case, you should still be able to import messages from the mailbox by manually selecting the messages in Mail, and then choosing to import the selected messages in M2FMI's main import window.
Hope this helps.