Dear user,
We recommend you to use AVS Video Converter to merge several video files. Here is the instruction:
http://onlinehelp.avs4you.com/AVS-Video-Converter/Features/merging.aspx
If the issue still persists please:
1. Send us the screenshot of Advanced / Conversion options window after you import the files to the programm;
2. Merge the two original files wich are out of sync after conversion and let us know if the issue persists;
3. Please make sure that all the files are played back correctly on the Preview
Best regards