When I use ff00ff on a background image for my systray, I get a black, non-transparent region where the pink should be. Is this something fixable, or does systray not support transparency?

Never have pink-magic problem with systray. What module are you using ?

i guess your SystrayBorderSize != 0
if it is so, then you must have this too in your step.rc:

Well, the bitmap I am using as the background is designed to expand, so the border exists. I have set it to FF00FF, but it still shows up black.

The module is the default one which came with the latest build.