Yes, I've found, in the past, that 100% of the time it's a margin issue.
Here is a simple solution, for those that make skins or are working on your first.
First, find out how big your taskbar is. Example: 23 px high. The tray icons, most of the time, will be 16 px high.
If you set the "top" and "bottom" margins at, lets say, 5 & 5. Add those together + the icon height, you'll get 26. You're trying to fit a 16 px high icon into a 13 px high spot.
There's not enough room for the icons to fit, so they won't appear.
If you set the margins at 3 & 3. Now it adds up to 22. Now they'll fit. Hope this helps. 