I just ran into the same issue. During playback, old effects played over the new effects. I went back and used Model --> Delete effects to ensure there were no previous layers remaining.
Then re-rendered. During playback I had both the new and the old effects playing on that model.
Rebooted and re-opened, re-rendered with same outcome. (Double checked that render was set to erase based on previous post)
This is on a PC, with windows 10. version .46.
Created a new sequence and imported the new effects with no previous effects showing up in the preview. I used import to see if there was a data layer in the model being rendered. But only the new effects were imported into the new sequence.
Not sure what else to try for reporting purposes.