I am a new user and have made some mistakes over the last month or so. I cannot solve your problem, but can share my conclusions. Musicbee is not itunes. It does not try and make decisions for you, but that means you have to read about it before you press its buttons!
I pressed buttons and had to start again twice!
I am just about getting to grips with it now, but am cautious because of the vast size of my music collection.
I think that Musicbee is going to be worth the investment of time, I have downloaded and tried about 4 others.
The previous comments mention the Inbox. I suggest you read about that and possibly start again! The Inbox is a great idea, because it is a holding bay for new additions. However, you can bypass it if you wish.