Problems after any firmware upgrade

Sincerely I don’t fully understand, help me to understand, what do you mean with “movie start menu” ? From my acknowledge the mkv format doesn’t permit a menu.

Maybe you wanted to say that the WDTV SMP stops the reproduction and brings you to the folder where the mkv file is contained?

In addition, could you please tell me the movies where you got this glitch, I would like to investigate on this. 

EDIT:  Did you have disable the header compression in mkvmerge?

Thanks