I just uploaded v1.3.1!
It is mostly a bug fix version, you can find detailed changelog in the post.
@lansing
I believe most, if not all, of the bugs you reported have been fixed in this version. Thanks for your feedback so far!
@rsotome
I reconsidered adding a re-muxing option, and I think that it is meaningless, since MkvMerge GUI does exactly what you ask.
Hopefully when v1.4 comes, it will include the batch feature that most of you requested. Thank you all for your support!