Dombral,
I did some investigating using Jim Kier's LWM Viewer & I have an idea what might be causing this issue.
The Surabays area in Onnogras' Java ports package contains 2 bgls of interest.
Surabaya2_3.bgl - this draws the land & watermask
Surabay2_8.bgl - this draws the roads etc.
In LWM Viewer they look like this:
So long as these files are present, & no other scenery has higher priority, the coast & land should match up well.
I checked the download here at SOH, & they are both present.
This means Surabaya should display looking something like this:
Your's obviously doesn't, so some other scenery bgl must be drawing over Onno's surabay2_3.bgl because it's higher up the priority (Sim loads & draws it later).
The only combination I can think of is either the surabaya2_3.bgl file is missing from your NEI scenery, in which case getting a fresh download should solve your issue
or...
The view above is taken from LWM Viewer. It shows Onno's surabaya2_8.bgl and cst4920.bgl from CFS2/SCENEDB/WORLD/SCENERY. This folder contains the default scenery for CFS2.
Your default scenery is loading AFTER Onno's, which means it's higher in the priority listing. Move the default CFS2 scenery to somewhere much lower in your scenery priority listing, so add-on scenery is loaded after the default scenery.
I hope this helps.