Can you zoom into one of these scene markers on your timeline and post a screen capture of that segment of your timeline to this forum?
Since you're using stop markers to return the viewer to main menu after each segment, I assume you've also got black video between each segment so that there is a second or two between the stop marker and the next scene marker. Is that correct?
I did have a blank frame between the stop marker and the screen maker, but I got rid of all the stop markers when I was getting errors in producing a DVD folder, and the DL DVD I produced had black menus for the later scenes. I still have the bit of the scene before appearing when I select a scene. I totally reset the menus after the stop marker problem, which has improved the performance of the program when dealing the menus.
Here is the screenshot. The marker is directly on the beginning of one of the problem scenes. When you select the Bell Tower scene you get about as second, less of the previous scene with the blue lake. There is no audio here. Some of the other scenes have a small sound but no video at the beginning.
And you still see a frame or two of the previous scene when you add a second or two of black between each scene?
Taking the video folder with stop markers out of the trash and using VLC I can defiantly see a bit of the old scene when playing a new scene, even though this folder had stop markers and a frame gap between scenes. These gaps were gaps in the timeline without any video. This causes an error to occur with the folder generation, and half the menus are black. The last visible menu has entries that don't work. After the black menus are encountered, it is impossible to go back to working menus. I can try adding deliberate black frames to the video to see if the previous frame starts when playing the current frame. This shouldn't cause the error since the timeline is continuous what this method, rather than discontinuous with the other method.
You should never have video gaps on your timeline! That will cause errors.
Any space between clips should be filled with Black Video clips, created by selected the option under the Panel Options (upper right corner) on the Project Assets panel.
Adding 12 frames of black video before the scene marker for the scene in the screenshot appears to have solved the problem. The other markers after it weren't altered and so have stayed where they are and the scenes have shifted. Maybe get rid of the black video and re-make all the shifted markers and hope for the best, this should solve the problem? Not only is the black video stopping the previous scene appearing, but the correct scene is starting immediately. The black video is evident in the scene before the current scene when played.
I managed to get a DVD produced with 5 frames of black video between the scenes I wanted. The Black Video made sure that the menu markers worked! The started at the beginning of the relevant scenes. I have never had to do this before in any program.
Adding stop markers didn't work. The menu markers would go to a point a half second or a second before the required scene, like having no black video. I have tried all sorts of things to solve this, even copying the project using the Project Archiver and opening the copy, but to no avail. I really don't know how ATR managed to get stop markers to work. I even added 12 frames of black video between frames with stop markers at the beginning of the black video and the scene marker at the end. This didn't work. I get nothing out. The program appears to create a folder, but there is no error message and no folder at the end. It writes date to folder far quicker than normal when using stop markers. Also the 12 frames of video don't work I think.
I have given up on stop markers. The normal use of the menus seems OK. Other programs like Apple Compressor have this type of menu structure.
Note using 5 frames of black video locks the menu markers successfully.