ApplicationMgr Return Code Fixes, master branch (2017.09.14.)

Making ApplicationMgr::i_startup() return a failure code in all cases when an error is detected. Previously it could in some cases return StatusCode::SUCCESS right after printing a FATAL message. In cases where the error was determined not based on a status code, but on some other condition. Making the sc variable actually be a success code in those instances.

This is a follow-up from !384 (merged), making sure that the issue found in there would not be lost.