Y have found an error in forced subtitles type "SRT", there are shifted.
Y've sent the bug to Handbreak and the last nightly build fixed the bug, ver: HandBrake-20161223-9e80492
In the version 2.40, y have always the error in the "SRT" subtitles. With HandBrake 1.0.0 all is ok.
Try 2.41. This version has HandBrake 1.0.0 core.
All is ok with subtitle "SRT" and "ASS". Big thanks