When I don't use my taskbar (When I'm using a program or AFK), stuff appears in my taskbar. First it's usually a folder (like a folder would appear in Windows Explorer, sometimes a bunch open up (stacked). Then application icons open (not actual applications, but what I associate with blank applications. When I click on anything on the taskbar, they disappear. When I woke up this morning, there were so many my computer was getting slow, and I spent over $1,000 on this 11 months ago. They appear over time (i.e. one after another, not all at once), so they build up after a while. Occasionally one will stack as if a second instance of it is occurring. In the picture, the stack of application picture has them all flat. It does that to them after you hover over them (and switch between them) for a while.
Although this has been gone over in these forums a few times since Win 8 CP came out, I shall attempt to help you.
These "empty" icons are generated when your Windows theme changes wallpapers. Hopefully this "bug" will go away in the final release. In the meantime there are a couple of fixes:
1. Right click on an empty spot on your desktop and click on the Personalize selection. At the bottom of the screen you will see the selections for your current theme. Click Window Color. One of the color selections on the resulting dialog screen is a multi-color fan icon. Click on that and save changes. This causes the Window frame color to change with every background rotation. The system chooses the apparent prominant color in the picture to color the frames. Yes, it can get some rather sickly colors at times. You can fix this by setting the color rotation in Personalization. This will fix the empty icons on the taskbar 99 % of the time. You may get occasional ones pop up, especially when your system comes out of sleep mode.
2. This method seems to fix the empty icon completely. In Personalization, pick the default Windows 8 theme that has the multi-colored fan on it. You will now need to add you own backgrounds to the theme.