Tom,
The cache tool is not able to build cache tiles for the extents mentioned in the error message " Failed to cache extent xmin ymin xmax ymax at scale xxxx". As these extents have missing tiles the cache status is reported to be less than 100%.
This can be due to failure to draw the images at the extents noted or due to data access issues. You can determine the problem by trying to draw the dynamic image service or Mosaic dataset in ArcMap at the extents and scales noted in the error message. If they do not draw successfully then check if the rasters that are accessed for those extents draw successfully or not.
Once you have resolved this problem, a re-run of cache tool should update the cache service status to 100%.
-Garima