<p>I had a similar problem: sorting by capture time, but one particular photo (stack) insisted on being at the start.<br>
In my case it was caused by external editing. It seems the filetype plays some part in the sorting: my file interchange type was set to TIFF. Once I set it to jpg (sufficient for my purposes) the photo/file ended up in the correct place.<br>
Hope this helps people with similar problems</p>