Trying to find a workaround...
My knowledge of SSH2 internal encrypted traffic pattern is not known to me and how SSH2 sets it's window settings. But I tried to see if I could change that of the Global Scape server by changing the TCP WINDOWS SIZE in it self. It did not work.
To try and see if I could affect the outcome I set some custom TcpWindowSizes in the Globalscape server we have. Apparently the EFTP server sets a the TcpWindowSize reg setting hard to 64240 instead of the windows usual auto window.
Neither changing it to auto window, 32786 or 16384 helped.
I'm actually only experinceing problem on Download from the server, not on upload. I can without a problem upload well above 50MB. This is of course valid from the description on the Putty page: https://www.chiark.greenend.org.uk/~sgtatham/putty/wishlist/ssh2-bug-maxpkt.html
As it's the server that will send to large packets.
Now I'll e-mail Mr. Prikryl and see if he is happy to provide 4.2 for additional testing.