This is more a note to myself than anything else (as will be most of this blog) but if you try to remerge MKVs and have seek / chapter change issues, there is this post I found which explains it and gives solutions.
My issues became apparent in both VLC and on the rapsberry pi (openelec 3.0.0 but I’m pretty sure any XBMC distros have the same problem) so the trick to fix VLC wasn’t possible in this case.
Using version 5.8 of the MKVmerge utilities fixed the issue for me.
Here is the link to the said forum thread: MKV time seek problems
And here is a link to version 5.8 in case you can’t be bothered: MKVToolNix 5.8