All uploads lack permission

All uploads with WinSCP are uploaded without proper permissions for some reasons. It's extremely time consuming to have to change permissions on thousands of files a day. Why can't they just inherit permissions from their parent directory?

Also, why does the properties dialog have options for Group and User permissions in 2 locations independently? It doesn't make sense. Even if I set the Group and user permissions to 755 I still have to set the group and user permissions in the drop down boxes above. I don't understand what that's about. Please help me understand this.

Sorry, but this is too broad question. A complete session log file would help.

Make sure you did not enable "Set permissions" option in transfer settings.
https://winscp.net/eng/docs/ui_transfer_custom

I'm not sure what you refer to by "2 locations".
There are ownership boxes (where you specify a username and group name).
And there's permissions box.

If your uploaded files get owned by "root", while you want them owned by a specific account, it must be because you are logging in as the root. Make sure you login using the account you want to own the files.