Do the messages all get colored brown in the mailbox?
When you select the good messages and hit Not Junk icon in the toolbar on the top of the Mail Message window, does the brown change to black? If you move it back to Inbox, does it stay there after moving it to inbox?
When you hit Apply Rules on the Message menu after selecting the message in the inbox, does it go back to Junk, or does it stay there?
If applying rules sends it back to junk, view Mail menu -> Preferences, make sure the Junk mail setting is setup this way, and go also to the Blocked setting to make sure messages from the sender you want to receive message from are not listed in the blocked setting. Then go to the Rule section and make sure no rule is asking messages of a certain sort to go to Junk. Keep in mind the Rule section follows boolean functionality