With the Pen Tool selected, check the settings for the Style and Width fields on the Properties panel. Maybe the values are not set to the default, regular stroke.
No all seem set correctly, I checked the hint box and that straighten it out better, though when you go to bend the line in-between two points its still doesn't behave properly!!
Is there a way you can share a FLA with this problem?
To share files as suggested above, upload your files to a shared server such as Creative Cloud or Dropbox and share the URL here.