There is a lag in feedback from Cigar Box. When you have finished your flight and clock stop, you will get Pirep ready, click ok and file the Pirep....done. Disregard any and all further popups. The Pirep files within a few seconds, but may return a time out etc. You usually have to restart Cigar Box for each flight. When using charter, beside to select and load the airplane first or you will have to re-enter the flight information.
Before also to select flight number if you are not flying a tour. For tours, select the leg in the tour center and then select get data in Cigar Box.....that should take care of the basics.