The issue is that they change the casing of the filenames to lowercase which corrupts the encoded filenames and prevents StockSubmitter from decoding them.
The only way to resolve this is to contact their support and ask them to make their system displaying filenames as is, without changing the casing.
It's only about the filenames, not extensions - if they need extensions to be lowercase (as their support says) - that's not a problem, they just need to keep the filenames in the original case.