If you have your master dark at the same time and temp as your lights, you can just use the Dark without a bias frame. If you do include the bias and the dark, you need to check the "optimize" button so that the Bias is removed from the Dark before calibrating the Lights. Otherwise you will end up subtracting the bias twice and introduce the types of artifacts you are experiencing.
As an aside, there are lots of places to look for help in getting started with PI. Harry's Astroshed is a great place to start. Also, I have a comprehensive cribsheet that I freely share. If you are interested, just drop me a note at jkmorse57@gmail.com and I will be happy to send you a copy.
Best,
Jim