New Key Signature Not Recognized??

So I'm transcribing this song that has several key changes, the first of them being Eb major going to F major. When I was finished the part of the song in Eb major, I went and I changed the key to F major, but even though both keys have a Bb in the key signature, and clearly the new key is F major, every single B I put in is going in as a B natural, and I shouldn't have to flatten the B every time if it's already in the key signature. Can someone give me some advice as to if I've done something wrong, as the new key of F major isn't even being recognized?

Also, I'm trying to add arpeggios/glissandi in my score, and all instructions just say to drag them in from the master pallate, which I've tried over and over again, but it doesn't work. Nothing happens. Any advice for this one? Thanks to anyone who can help me.