Hi,
Thank you for reporting this. We found the issue. After the form restructuring in 6.4.0, file uploads via custom item fields on the product page were not being saved with the order. The uploaded file reference was stored in a hidden input that was missing the link to the product form, so it was not included when adding the product to the cart.
We have fixed this in the latest update. You can download it from your member area and install it over your current version. After updating, please clear your browser cache (Ctrl+Shift+R) and test the file upload on your custom label product page again.