Well, first of all, excellent troubleshooting. I was already on my way to test if the quoted filenames had anything to do with it...
I had also noticed that the desktop doesn't like to drop files anywhere, and sticks to the grid order which I remember other people complaining about (and here's another good reason for it). So I'm actually bookmarking this thread for future reference, I'm sure it'll come up again.
Don't worry too much about it, that's just the Linux way! And trust me, it will happen again...
Here's me taking months to realize that 40 is bigger than 4 