It's not possible to leave remnants that won't go away when you render *UNLESS* you've got your Render Mode set to "Canvas Mode" so check your Settings.
So I hadn't even ran across the Render Mode settings until I saw this post. I just checked and mine is of course set to the default which is "Erase Mode." So, I then went and looked at the manual to get a description of the two modes. The manual explains it very well and is exactly how I have gotten rid of remnants when I have deleted effects. As Gil has mentioned, I would suggest you try and re-render your sequence and see if that fixes your issue.
Here is the part of the manual that deals with Render Mode:
If the Render Mode is set to Erase (which is the default value), then the fseq file is erased before every
render. If set to Canvas Mode, then the data in the fseq is not cleared before a render, rendering is
done over the old data.
Note: If set to Canvas mode, deleting an effect will still show when played until it is overridden with a
new effect. Imagine a 6 foot painting in which you paint over a 4 foot section. The 2 foot original section
is still visible. This is the how canvas mode works.