If it was just FREEflow New England (or any other corrected water scenery) there wouldn't be shorelines out in the water like that.
What would do that is a combination of FREEflow New England (or another corrected water scenery) plus another scenery (Logan Airport, perhaps?) that's either:
- intended to work with the stock scenery, or
- the reverse - no corrected water scenery but another scenery that's meant to work with corrected shorelines.
Some scenery includes its own shorelines, and they would be set up to work with either the stock shorelines or a corrected water scenery, but not both.
One way or another, it looks like there are a couple of incompatible sceneries installed and active at the same time.
Edit: Another possibility occurs to me. Maybe if there is a corrected water scenery link FFNE and a Logan airport scenery that has its own shorelines, perhaps the airport is below the corrected water in the scenery stack when it needs to be above it?
2nd Edit: I have FFNE in GW, and I installed a Boston airport scenery that was designed to work with GW and the stock shorelines. It looks rather like what I see in your screenshot. I installed that airport and had to make exclude files to get rid of a few misplaced shorelines that were out in the water like in your screen shot, but I only had to get rid of a few little bits of shoreline, not big sections like you have. Still, it might be the same sort of issue but not the exact same scenery.
And yes, the stock shorelines really are that far off! I know this from the way the stock scenery depicts lakes and rivers in my home locale in western Mass, where some lakes and ponds are incredibly inaccurate.