I did the sequence: load image (JPEG 1760x1168), crop, scale 
(shrinking), save, scale again, save-as, close image window.  There 
were 20 images and I did all of them in one execution of GIMP.
    Starting with the seventh image and for all further ones, there was 
an anomaly in cropping. Cropping appeared to happen in the image 
window, and the previews cached in ./.xvpics were cropped, but the 
saved main image was not cropped, showing the whole image, and the same 
for the second scaled version.  Scaling did happen, and if later I 
reloaded the incorrect images and re-cropped them to the previously 
selected boundaries, the image size was what I planned to have, i.e. 
scaling happened and was correct.
    Most of the images were worked on just as shown above.  In a few I 
used image-color-curves (value) to adjust contrast, after cropping.  On 
the fifth and sixth images I tried some fairly complicated operations 
involving adding a layer mask to the background, and adding another 
layer to one of the images.
    When I exited from GIMP it complained "swap file not empty".  
    Another time when similar failure to crop occurred, I believe there 
was no "swap file not empty" message, but I did do some extensive 
masking and layer manipulation at the point where the cropping stopped 
happening.  Except that time, just one image among the non-cropped ones 
did get cropped.  I did the editing in several sessions, and I cannot 
guarantee that I didn't do layer operations on the first image of a 
session.