It's difficult to advise you on this one because you are describing a printing strategy that makes little sense and the desired results could probably be achieved using a more standard approach.
1. The general rule of printing is to always print the lightest color first proceeding onto the next darkest color with the second pass etc.
2. It is also assumed that the paper or film is white although thermal printing allows one to print successfully on colored substrates. Doing so, however, calls for observing certain changes in technique and limitations to what one can do.
3. Generally speaking, print order and the proper use of the Overprint and Overlap parameter settings is all that is necessary to achieve any desired result. In 18 years I have never found a need to use the Layers feature in Omega nor have I ever found a need to print white foil on black vinyl.
So please explain the following:
Why are you printing on black vinyl instead of simply printing black on white vinyl to start with?
Why are you printing from more than one layer?
Please also post some images of your setup and of the finished print. If you want to send me the PLT file by email attachment, I can also better understand and help you. My email address is in my signature beneath this post.