I talked with @evanweaver about this. We know this will just be known issue for now, it is a complicated fix, the preferred solution maybe keeping the header row always visible so scrolling isn't necessary. We should note this in release notes so people know how to get around it.
Issue: If select an object (hilighted in yellow as copy object for "Apply to Selected" and then use the scroll bar to go up to the top (if header row is off the screen) you lose the selection. I also had the same issue using the mouse scroll wheel. The work around for me on windows was to use the "up/down" arrow keys. That allowed me to get back to the top without losing my selection.