Generate score - MIDI Files?
The "Generate score" item of the "Edit" menu has the purpose to compute the score according to the composition blocks of Pizzicato. It was never expected to be used to transcribe a MIDI file into a score even if, in version 2, in most cases, it was acting like this. Version 3 is slightly different and it does not work for that purpose.
To import a MIDI file and display the score, you should use the File, Import MIDI file... menu. Then select all measure (Edit, Select all) and transcribe (Edit, Transcribe).