I just tried version 5.2.0 build 2756, and it works great! No more popping up.

Thank you very much!

I have sent you an email with a dev version of WinSCP for testing to address you have used to register on this forum.

This issue has been added to the tracker:
https://winscp.net/tracker/943

I can see the same behavior in 4.3.9.
(Not that I'm defending it).

Version 4.3.9 (Build 1817) works fine. It doesn't pop up anything.

I click the "Keep remote directory up to date" button, then I click "Start". It does "Comparing" for a while, then the "Keeping remote directory up to date" window sits there watching for changes. Then I click "Minimize" and it all goes away. This all works fine. But at this point, when I change a local file in a different program and save it, a WinSCP window briefly pops up saying it is copying or something (it happens so fast I can't read exactly what it says). The file copies fine, but that window popping up is really distracting. It didn't used to do that.

I'm using version 5.1.0 (Build 2625). I don't remember the previous version that worked correctly. It was probably the 4.3 branch. I'm going to switch back to that version until this is fixed.

I was scp'ing to Ubuntu 10.04. I'm using Windows 7.