If I understand you correctly you have created a bootable USB stick with the new Navigatrix version (0.5) by using the Windows Start-up Disk Creator (the second downlaod from the "Download" page)?
(1) Have you already checked that the ISO file has been downloaded correctly? Boot from your "old" USB stick (version 0.4), open the file manager, and navigate to the folder on your hard disk to which you downloaded the 2GB ISO file. Then press <F4> to open a terminal window and at the prompt type
Code:
md5sum navigatrix.iso
This will run for a while and then print a 32-digit string. This string must match
fc2e1f867d0c98a157074292d9ce04ed for the most recent ISO. If it doesn't match, you'll have to re-download the ISO file.
(2) If the MD5 sum is correct, could you try to create the "new" bootable USB stick from Navigatrix rather than doing it from Windows? Boot from your old Navigatrix USB stick and, in the File Manager, go to the directory on your hard disk where the ISO download is stored (this is just to make Navigatrix "connect" to your hard drive). Then, in the Manta Menu, go to Preferences -> Startup Disk Creator. This application allows you to create a bootable USB stick from the ISO image file that you downloaded.