Hey Leo and Kerim,
We’ve been having similar issues today importing FAB scripts to Encore CS6. Actually, the lines for us appeared in the Monitor and Preview as well as in the outputs.
After speaking to one of Adobe’s support techs, we tried importing the subtitles to a brand-new project with only the one relevant timeline; all the lines disappeared.
With a bit of wrangling we found success with the following steps:
– Open the project
– “Save As” a new project
– Remove all the old subtitle tracks
– Import the new FAB script
The lines haven’t reappeared for us yet. Hope it helps for you as well.