I remux all my mkv to mp4.
I have played with several sections of the profiles.conf and mcebuddy.conf in the past and up until the last two releases (I think) of Buddy my remuxed mkv are the same length as my new mp4.
Now not so.
Are you sure fixed up the profile.conf and mcebuddy.conf after updating it?
Yes I have and always check the 2 conf files.
This has always been an ongoing issue for me.
Why are these settings in the conf files anyway?
Can I take them out forever?
These settings are included by default because most video have corrupted timestamps at the beginning of the file which leads to audio sync issues. Hence by default MCEBuddy skips over the first couple of seconds.
If you videos are of good quality with no corruption or timestamp issues you can remove these settings from your .conf files but note that you will need to do this after each upgrade since the files are replaced during a reinstall.
If you want you can attach your conversion log and we can take a look and let your know what’s going on.