OK, that's odd. A dock mask for the iPhone 5, for example, is 118x120--it's not like it's full screen. I'm not sure how it could possibly affect the undocked icons.
Which dock/theme are you using that does this?
Regardless, Frenchjay's suggestion should work. If need be, put the reflection in its own theme, and place that theme above everything else in Winterboard. That will override the problem if there's another dock mask hiding in one of your theme folders. Make sure to toggle both themes in Winterboard, then respring--that can help when cached images resist changing.