Keynote movie playback ignores start/stop times, only in presentation mode
Since you have set start and end on the clip, Keynote can permanently clip it after reducing file size to save space and improve performance.  The result is that the undesired parts of the clips are no longer even available to Keynote so they shouldn't play when looping.


Set your start and end points
Go to File > Advanced > Reduce File Size


Keynote will trim the excess footage from your video file.  You will note the change if you deselect the video then select again and view the Edit Movie in the inspector.  (Be sure you keep the original somewhere else as a backup.)

Before:



After: