Congratulations Harmy!
@ analog: What authoring software are you using currently? I ask because I'm also tinkering with making a Blu Ray as well (didn't know anybody else was, whoops), and I ran into issues with subtitles as well, and it appears to be what Catbus was describing. I muxed the disc without subs successfully but when I added all the subtitle tracks I got multiple errors telling me the data rate was exceeded. The software I'm using (Sony DoStudio 4.0) only allows image-based subtitles however, so unfortunately the only solutions would either be
a) regenerate every sub at a lower resolution (I used the 720p version in Project Threepio), although since they're already cropped to their minimum size I'm not sure how much difference that would make, since I'm 99% sure it's total image size that matters rather than resolution.
b) cut out a subtitle (or audio) track and remux until it all fits
As nice as it would be to have everything from the MKV download in one place I'm just not sure it's doable given the limitations of the format.
Any chance you'd be interested in collaborating? My Photoshop skills are pretty limited but DoStudio is very open-ended, so the menus can be programmed in any way you want, which would be useful since there are SO many tracks to choose from. Shoot me a PM and I can send you some examples of my previous BR work if you want.
edit: saw you had issues with chapter markers as well, in DoStudio they can simply be imported as a text file with the timecodes in it, if that's also a selling point :P