In lsxcommand, when you type the beginning of a command that is already in history, it "autofills" the rest of that command and highlights it. Problem is, this highlighting is opaque, as in it's over me text and I can't see what I'm writing. I'm not sure if this is clear, I could a screenshot if anyone asks for one...
I have a feeling you're misinterpreting what you're seeing. There's a bug in lsxcommand that sticks a lot of spaces at the end of history entries. When these are used in autocomplete, the spaces cause the line to scroll, so you see the box filled with highlighted spaces.
I don't think anyone has been able to find exactly what is causing this though, which makes it very hard to fix.
Ouch, that sucks. Thanks anyways I guess.