I have set up a number of transactions as bills. When I have paid the bill it then appears again as a minus amount with applied in the status column. is this normal?

Yes it is perfectly normal. You will see the same thing in a customer register with Invoices and Payments. 

The supplier register you are viewing is just a list of transactions of multiple types and one cannot sum the column to mean anything. Actual reports, however, will be correct. Even though a bill and a matching payment both appear negative the supplier open balance will still be null.