You didn't mention the caliber you are having the problem with. My problem was with .223. I would get an upside down one every 20th case or so. I got on Dillons forum and asked about it. Dillon was responding, but didn't have an answer. Another forum user suggested moving the little metal plate at the case feeder opening on top to close the openeing a little. I closed the opening about 1/8th inch and now I get no upside down cases.
Load up the collator bowl with cases, set the drop tube up so the cases will fall into a bucket, turn it on and watch it's operation. Eventually you will see what is happening differently to cause the upside down case.