I use motion menues in every Blu-ray project i do and stopped using the Loop Point feature for some years ago. I use the fade up video in a Menu as First Play and set the Loop to None and then set End Action of the intro to the main menu. By doing this i don´t have to use the Loop Point feature.
By doing this the glitch caused by the Loop Pint feature is gone.
Intro in a separate file+menues in a separate file/s is the way to go if seameless menues is your goal.
EDIT:
If using the Loop Point: Be aware of that a Loop Point always must point at an I-frame. So if your transition ends at 00:00:05:00 the Loop Point can´t be set to 00:00:05:00, it will find the nearest I-frame which is either 00:00:04:24 or 00:00:05:03. I have a gut feeling that your Loop Point points to a point where the transition has not finished, thus the issue. No matter what, using the Loop Point feature will never create seamless menues.