Need help to overcome merge sound "BEEP" problem.

I can merge two different mpg's with TMPGENC Merge & Cut option. It works but i have a problem with the sound. Exactly where the merge takes place a "BEEP" / loud click sound is introduced.

I have a few different mpg's that make a complete movie. At all the merge locations there is this "BEEP" sound introduced for 1 sec.

Please help with any ideas. I need to get this done.