A couple week ago I had written about "Host is not communicating for more than 15 seconds. Still waiting..." problem.
Here is a screenshot from an operation: http://4.bp.blogspot.com/_JPKqDqb78z4/TK3x9It95SI/AAAAAAAABYw/6QFFJEQDSWI/s1600/WinSCP_Abort.png
What's happening there is this:
I have a NAS (QNAP) and in that box there's a SVN folder which contains close to a million small files.
I tried to get a copy of the folder using SMB (samba) or SFTP/SCP/FTP but they were all hopeless --would have taken weeks.
Then, as another solution, I connected a USB HDD to the NAS.
I am using WinSCP to copy that SVN folder to USB HDD.
Trouble is, WinSCP keeps popping up the above dialog box.
Not only is it very annoying, it also makes it impossible to minimize WinSCP.
Here is my suggestion:
Since the copy/move dialog is a custom one (i.e. it's not dialog from Windows), could you add this "Host is not communicating for more than 15 seconds. Still waiting..." message to the copy/move dialog too.
If the user chooses to stop the operation s/he can always click the 'Cancel' button on that dialog.
Or, opt to press 'Minimize' --like I would.