Putting the issue here as it's definitely a Garmin Connect back end issue.
Since some time the elevation corrections are enabled by default for all uploaded activities (I have a fenix 5). In addition, data from CIQ fields, although present in the FIT file, are not shown on GC.
This is a well documented issue:
https://forums.garmin.com/forum/on-t...d-reference-id
https://forums.garmin.com/forum/into.../138105-/page2
I have also tried to upload a run from where all was working as expected (I have the original FIT files) - after re-uploading the same file, the elevation corrections are enabled. That 100% confirms it's a back end issue and not related to anything on the watch at all. Interestingly, when the file was uploaded originally, the software was reported as 4.10.0.0. Now, after reuploading of the same file, the software is 4.4.0.0. This allows me to pinpoint the date the issue appeared to between 23-29 July 2017, when my "4.10" started to be reported as "4.40" (there was no such version in fact) and the issue appeared.
Lastly, exporting the original activity file from Garmin Connect for an activity uploaded before this issue appeared downloads a file which, when reuploaded, results in an activity page with the issue again manifesting itself.
I am awaiting Garmin to get back to me on an open support case.