Sometimes, but not always, when I edit a jpeg (it may be as simple as changing a keyword or rating), Lightroom will clobber the capture time and overwrite it with the current time. After this happens, the original capture time can't be found anywhere in the EXIF data, except in the GPS timestamp (it's always happened to me with iPhone images, but I don't edit any other jpegs regularly). Strangely, those images still sort in the correct spot when sorted by capture time, so the original timestamp must still be in there somewhere.
Has anyone seen this before?
The only way I can think of troubleshooting that is to save the original .jpg before you import it, and then save a copy of the .jpg after the problem occurs. Then we can compare the metadata of the two files to see what might be going wrong.