Non-spam is moved to junk folder

Spam and Junk are two different beasts. If you do get anything that is labelled Spam, then it's being done outside of Thunderbird. Junk classification is done by Thunderbird, using a scoring system based on analysis of the frequency of words in incoming messages. One choice is to train the junk controls by marking messages as Junk or Not Junk manually. Select the message, right-click and look for Mark As, or use j and J - I think j means Junk, J means Not Junk. Your other choice is to disable the junk controls; look under Account Settings. You set it independently for each account.