H.264 stream does not contain fps field

Hi, I've been having some sync issue with some hdtv programs converted to mkv, when encoded to dvd there always out of sync, i've found a long and laborious solution but found this with tsMuxer.

When i used it to test the mkv files in question and converted them to AVCHD they were also out of sync, i noticed this: "H.264 stream does not contain fps field. Muxing fps=25", 25 fps is correct for the files.

Could this be the cause of the sync issues and can i add the fps field to the 264 stream. The files are constant bitrate, just wondered if anybody could help with this, thanks.