It is not during any encryption in advance, so I do not know that is the problem. I have never experienced this problem.
I have only one hint, but I do not think that it will help:
If you attempt to transfer very large file using ASCII (text) mode, it is converted in memory before transfer. It may take a long time.
Actually that hint solved the problem. The files we were transfer were large lists of user ids in txt form. Switching the software to always use binary made it work. Thanks.