There're a few of redundant options you're using on x264 and mkvmerge that you don't really need to.
In the full help of JEEB's build, only 2 lossless possibilities in the audio section --acodec :
copy source without transcode (good for FLAC)
specify codec (ALAC and PCM only...)
Using "--acodec copy" results in :
mkv [error]: unsupported audio codec
I'll stick to the vanilla builds for keeping FLAC until new builds fix this.