This has happened a few times in a past, then went away, now in last two Lightroom CC releases happened again.
Basically I am sorting out my photos by capture time (older to more recent) - that works fine by itself. I also do a lot of file selection and panoramic stitching in Lightroom directly, which ends up creating panoramic raw files. The created panorama raw files take the capture time from the last photo used and, when added to Lightroom, used to go after the last photo used for panoramic stitching. Not anymore - since last two Lightroom CC updates they annoyingly get inserted before the last photo in panoramic sequence which is quite annoying really. This makes it quite difficult to deal when processing the shoots with quite a few panoramic sequences.
I am guessing it has something to do with secondary ordering when the timestamps of the capture are the same - that secondary ordering is not available to user and it seems that software keeps changing it. I'd appreciate it if that could be fixed. I am using Lightroom on MacOS (latest version of OS).
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Please update Lightroom to 6.9/2015.9 version which includes the fix for Lightroom CC: Messing up file ordering with panoramas | Photoshop Family Customer Community