Check that the access rights are consistent.
Make a note of the "rwx" privileges for owner, group and world on a file that is displayed and one that isn't. If they are different then make the them the same - i.e. the value of the file that is displayed.
Also check that the directory/folder access rights are consistent.
Check that the pathnames to the files are correct.
Case shouldn't matter, but double check anyway. Check that there are no unescaped spaces or other special characters. Either rename the files or change how they are referenced.
Double check the colour mode of the files.
Some graphics packages can write CMYK jpgs as well as RGB ones. Not all browers (eg. Internet Explorer) can display CMYK jpgs. You'll need access to Photoshop or similar to check this. Resave the files in RGB mode.
It's unlikely to be this given you say that the problem has only started since an upgrade, but I've included it for completeness.