Note that FileZilla always uses a transfer queue with multiple connection. While WinSCP does not for the default foreground transfers. You might want to use "background transfers" to use multiple connections.
https://winscp.net/eng/docs/faq_slow#transfer_queue
If this does not help, please post session log files both from WinSCP and FileZilla.

Hi there,

I switched from FileZilla to WinSCP. So far so good, but what is the thing, with the upload speed? I need to transfer WordPress Installations from time to time, so many single files. A recent example: ~ 7.000 Files, FileZilla does the job in about 9 minuets without any error, WinSCP says it needs three days (!) and 19 hours. I have 50 mbit/s upload...what can I do to improve speed? It is unusable like this.