I can tell you what I did to solve it?
For each affected file, From the menu click Image/Convert Image Colour Space, and it brings up this box here:
Convert Image Colour Space.jpg
Leave everything as-is except the selection in the Depth drop down box I've opened up just there. For some strange reason Krita seems to default to 32-bit integer/channel - even if you alter the app settings to try and force it to use 8-bit integer/channel depth (the only one of those four options that will easily save as a jpeg).
Its pretty annoying, but once you set the depth right for an image it seems to stay ok after that
EDIT: I took so incredibly long sorting out the screen shot that you ninjad me Red - again! LOL!
I think, from the solution I managed to work out from the error messages I got earlier today (as shown above), its about bits per pixel.
I've tried adjusting the settings to create all new files with only 8-bit depth, but even just preparing that screen shot within Krita itself I had the very same problem - it required converting from 32-bit to 8-bit.
I'm beginning to think that there's a bug in the software, where the software doesn't necessarily obey the settings panel. But its no biggy now I know what its doing and how to put it right. I'd be far more upset if I'd paid for the app
EDIT2:
These are the two error messages you get if you are in 32-bit mode and trying to export a jpg.
error messages.jpg
And this is the result of that happening
32 bit.jpg
And that's the same image as in post 14 above. Plays merry hell with the water!
EDIT3: PS - Falconius - if you convert a file to 8-bit when you've been working on it in 32-bit you may have to adjust the transparency levels of most of your layers, as the effects are much less subtle in 8-bit mode! I try to remember to convert before I really get started