Make sure your death magenta's actually RGB(255, 0, 255), it won't accept any threshold of colors that are approaching it. Unless you're running Verge under a 16-bit color mode on Windows, but that's just silly (especially since it'd only look fine on your computer), and that's entirely just a side-effect of color loss (only having 5 bits for red, 6 bits for green, 5 bits for blue and Verge just scaling 32/24-bit color (but alpha channel isn't used), which has 8 bits per channel, into this depth). Verge and MapEd just check for death magenta, it doesn't do anything like detect anti-aliasing for you.

Additionally, the bottommost layer does not get transparency because it's supposed to be treated as a solid background. Make sure you weren't trying to place transparent tiles on that layer. (In the editor, they'll appear with purple if they're drawn on that layer, but appear normal on any other layer)