I'm experiencing also random freezes. I can't discover what is the exact cause, so I can't reproduce. I start an upload session, queue a lot of files and let winscp work in the background. Lately when I switch back, it's non-responsive.
It's interesting, in the majority of the cases, winscp is still working in the background (uploading) so I let it work. Since I'm in trouble when I stop the upload (half files are still taken and processed by the stock agency) I wait until all the downloads are finished. To know this, I check the network activity in the win. task manager, after this End task for winscp.
The problem my rise if I minimize winscp before let it work in background.
As soon as I will know more about freezing I will post here.