Yes usually uploading images does not read the metatdata and rotate the images according to the orientation flag in EXIF data. You have to manually rotate the image before uploading. Had a lot of fun until I realized that...
Under Linux I use either the command line tools imgagemagick or jpegtran, which are available for windows too, but cumbersome to use compared to the usual windows tools.
For advanced editing I use GIMP
https://www.gimp.org/ it's a free photoshop alternative and has a quite steep learning curve, but you can do a hell of things with it.
Easier to use viewer and converters are either irfan view or xnview. So you don't have to rely on the standard windows tools which sometimes work as expected and sometimes not...
So good luck, but I think something different than the usual windows tools might help.
poppy