Well something is different.
The source file is fine.
Meaning the m4v, before import to Encore, plays from the beginning, using what software?
What happens if you import that m4v into Premiere?
I'd compare the problem file with a "good" one in gspot or mediainfo.
Gspot: http://gspot.headbands.com/
Media Info: http://mediainfo.sourceforge.net/en/Download/