I'm using win7 64bit, winscp commander interface, select a lot of files and upload them by pressing F5.
Then I open a new session (let's call the first session A, the second B), select another files and start uploading them.
Now every time an upload finishes in session A (the hidden one), in the system tray a message bubble pops: "Session_name: Transfer queue is empty", however the queue isn't empty, the upload continues with the next file.
If I switch to session A, messages begin to appear from session B, every time a file upload is finished.