Source material goes off a frame when making markers

I have made many attempts, even has teachers from universities puzzled.

I have a video with many scenes, its 29.97 frames. I need to edit it and move things around, so I made a sequence with a matching frame rate. I use markers (in and out) to insert the part into the sequence.

The problem is, when I cycle through the start frame or end frame it is sometimes wrong.

For example one scene ends at 00.29 and the next scene logical starts at 01.00 according to the source time code. but when i place it, it will have the last frame from the other scene at the start. this is extremely frustrating! Then when i come back to it the source time code has changed to the right one?? I know this because I wrote all the time codes into a spreadsheet. I really need help, my work is due very soon!