When TotalFinder starts up, the DS_Store files/icons that exist on my desktop go invisible but still have a “physical” nature to them that still registers as a file (albeit hidden) when automatically sorting files on the desktop.
This is reproducible each time I restart Finder and then launch TotalFinder, as captured in the following video:
Thanks for the video. I can confirm this issue and it has been on my list since Mavericks release.
We were forced to re-implement the original “NoDesktopDots” feature under Mavericks, but our new approach is problematic. It does not remove dot files icons, it just skip their rendering. That is why it is creating “holes”.
Now when I have better understanding of Desktop Finder internals, I’m going to investigate new and better implementation.
Found a solution. Looks good in my tests under 10.9.3. Hopefully it will be stable enough and won’t introduce any problems.
Will be available in the next release (1.5.34).
That’s great! I look forward to the update…
This has been fixed and I love it. Awesome!
Thanks Antonin,… but not so fast… 
See above video… still having issues.
Thanks for the video. I will look into that.
@mkormendy I wonder how did you copy (or paste) those files on the Desktop. Thanks to reports of other people I found pretty severe issue in my implementation. I hide icons when I detect that their name starts with dot. The problem is that some tools copy/move the file first with dot prefix and then rename the file by removing the dot prefix. For example standard screenshot app does that. My code did not detect renames so the icon stays hidden because initial name was with dot. It creates ghost placeholder.
This fix will be in 1.5.36, but I’m not sure if it will resolve your issue. I would like to find a way how to reproduce it.
@darwin i was able to reproduce this issue by visiting a website in google chrome that allows me to view a pdf from within the browser using chrome’s native in-browser pdf-viewer. The problem occurs specifically when I save the PDF to the desktop. See the video below:
Thanks for your detailed info. I have just tested it here and I can confirm it is the same issue. Chrome creates a dot file first and later it is renamed to a real name.
This bug will be resolved in 1.5.36 (hopefully released today)
This issue is occurring in latest 1.8 on ElCapitan. To recap the .DS_Store file icon is invisible but taking up physical space on the desktop leaving a gap, over which other icons cannot be placed.