Sorry, I haven`t seen your question earlier.
I had exactly the same problem. There is no need to edit the files manualy.
In my case the problem was gone, as I checked "objects as obj groups" * in the blender export options.
greetings
*Edit: Sorry. Donīt check "material groups". Was a mistake of mine.
**Edit 2: After some testing it seems that sometimes is nescessary to check "material groups", sometimes not. It worked fine for me to have both checked , but now I stumbled upon a modell - the NLGH lightship - where checking "material groups" during blender export messed up the whole texturing after reimporting in S3D.
Perhaps someone has more knowledge about these things?