Just a hunch that the sequence was configured for 100ms or 50ms timing.
The timing "resolution" will need to go to 25ms in your sequence to get the imported marks to match.
Even with 25ms timings, the imported marks will still be adjusted to the closest 25ms interval. This is still a huge improvement over 3.x where we had a 50ms skeleton.
Go to Settings, Sequence settings, bottom left will have the Sequence Timing resolution.