I agree that it would be good if the speed slider could be enabled for background transfers.
One weird thing about WinSCP is that you cant regulate the downloading speeds when the downloading takes place in background (in the queue window) compared to downloading "not in the background".
There really shouldnt be that huge difference, becasuse for software user - downloading means downloading - he isnt interested in that applying the speed restricting extra functionality in queue GUI might be for programmer annoying task.
I think it is better to have that feature working in all cases.
It will be improved eventually.
You can choose the upload/download speed in WinSCP using a percentual slider. But how exactly does it determine the maximum speed? Whatever the method, it doesn't work correctly in some cases.