I'm using Sublime Text (OpenGL mode) on Windows XP. Perhaps Windows Vista or 7 fixes this issue...
When I'm using Sublime Text overlapping other windows which use transparency effects, I get a lot of bleed-through artifacts in my Sublime Text window. For example, turning on the "Main Window Transparency" option in foobar2000 and then positioning it under or over the Sublime Text window makes all kinds of weird effects happen.
Other programs which use transparency effects cause the same issues. Metapad, for example, on which you can set the global transparency, causes its window area to bleed into the Sublime Text window.
Here is a screenshot, showing the issue with foobar2000: greywyvern.com/tmp/sublime-transparency.png
I am using the program with the --opengl option.