That's strange. I've remuxed 4 BDs int mkvs with the raw .sup file and all of them works fine. Are you using the latest version of your tools (mkvtoolnix, matroskamuxer, eac3to, etc.?)
I think it should be fixed on mpcsubs.dll because when i try with ffdshow engine from ffdshow patch, i have the name from MPC Matroska Splitter but like ffdshow recreate IAMStreamSelect Interface with information from Pin out of splitter. I'm a little disapointed lol.
Mpcsubs.dll take source from mpc-hc team and with mpc-hc player and MPC Matroska splitter we didn't have the name too so i don't know if it's on mpc-hc sources or cpp2005 sources
But we know that cpp2005 can try to fix it thanks to him, i have try to look but my knowledge is not like cpp2005
Thanks