Ok, I tested out sveakul's nifty search link and didn't find anything, so I'm making a report. Not sure if this is just 3.6, but it's been happening for at least the past few months:
The warning you get about losing the folder structure when moving files by drag-and-drop ("all the dragged files..." etc) comes up almost as many times for me as there are files. I moved 41 files just now and counted that message 39 times. Maybe it's only repeating per folder? In any case, it seems like once should be enough.