Maybe this will work for you. I used it with my PS3 with DVD5 and DVD9 discs..
If the output index file index.bdmv shows a value INDX0200 at the beginning then try a program called AVCHD-Patcher 1.06 and run it. It will patch the address of the Index and MovieObject.bdmv files to INDX0100. It creates .bak versions of the original files so you can compare.
The output from TSMuxeR and older versions of BDRebuilder to (DVD5 and DVD9) disc, ended up as a data disc until I used that patch program. I believe the newer version of BDRebuilder applies the patch automatically. Anyway it's easy to check these 2 files in a hex editor and the change can even be made manually without the patch program using a free editor like XVI32. You can view it in notepad but I don't suggest applying any changes with notepad.
I can't confirm that this works on BD media but with a Blu-ray structure on DVD media it works on a PS3 with all the menus including audio and subtitle track selections.