Good morning!
I have just tried BPP with your data. By clicking on "Add Files", all the files are automatically selected as master bias, master dark, master flat and light frames, with the correct filters. Then the script works without problems to calibrate, register and integrate the nine light frames, generating the three corresponding master lights. See the attached screenshots.
Are you selecting the Use master bias, Use master dark and Use master flat options (right panel)?
(NB: Note how the default pixel rejection parameters have been useless in this case. Obviously, with just three frames the default Winsorized SC pixel rejection is a bad choice, but this is a good example of why I added the warning dialog about integration with the BPP script.)