In the attachment you provided there is this line:
UE4Editor-Cmd: [2018.03.04-07.15.17:415][ 0]LogInit:Display: Failure - 2577 error(s), 3698 warning(s)
2577 errors. So read your log and search for this errors. I’m pretty sure they are related with the file names too long. I don’t think that Substance is causing troubles. There is nothing in the logs about it so should be ok. The engine is built automatically when you make a package for the first time or when you perform a full rebuild.
If you are using the project launcher, you can make a custom launch profile in which you can set “Build” to true. Anyway I suggest you to try with a normale package until these problems go away.
Fix the file name problem and let me know if something changes.