@cmuzzini The links you shared don't work. Please attach your files directly to this page.
Notice that old binary *libraries* are not compatible with the conversion tool and won’t load at all.
However, old *programs* saved in QuickBASIC 4.5’s quick save binary mode will be converted successfully in most cases.
If the binary is from QB7.1 or even VBDOS, the binary save formats were different and won’t load at all, and you will need to be running either QB7.1 or VBDOS under DosBOX to convert the files to text mode yourself, as stated by Richard.
All that said, if you do upload the faulty files here we can have a peek and try to help diagnose the case.