I've seen this happen after Gwenview edit (windows x, slackware 13.37).
The image appears to be back to its original rotation.

Is it just the fact that the thumbnail has not been updated properly.

(now I know this will get me a heap of rage)
But I've an iphone and a program (square ready) sees the image as unformated (cropped in normal picture editing), now I know you may not think this is related, but perhaps it is.
[Just found out this is a known iOS issue]

Don't jump on me for iphone using.(cause android programs don't work consistently - cause linux has NO uniformity between versions - now I HATED iphone & apple, but they are single focused and what they do they do well - everything works, reasonably well )

I love Linux btw, but they need to well, ya know, concentrate a bit more on a few OS's. and end Dependency hell (lets all go back to just making programs from C ).

first you really DO NOT want to resave "lousy" compression jpg's as jpg's

you are going to be adding in even MORE compression artifacts -- basically removing ( deleting) information in the image

use a LOSSLESS format until you are done

then save as a jpg but with 95% to 98% of the quality ( do not use the default 60% quality)