It has been working just fine until the other day.
Something must have changed for this to happen.
If you did not change anything yourself, then check to see if any automatic updates to your Drupal installation were installed.
Also, check with your web server to see if they have changed anything recently (such as upgrading the version of PHP installed or changing any PHP settings) which may be contributing to your problem.
It would be much easier to troubleshoot your scenario if you were able to provide the URL to the gallery in question so that I could take a look for myself. Without seeing your gallery's embedding code, I have no way of knowing how the path to your gallery's XML file is defined.
It sounds like the PHP file within the Drupal module which dynamically generates the XML data may have somehow become corrupt or missing but, if this were the case, then re-uploading the module's files to your web server (which you have already tried) should solve the problem.
It doesn’t mention what to do with images/ , thumbs/, config.xml, index.html.
These files and folders are unique to each individual gallery and it is not necessary to copy them into the module's own file structure. (The module deals with these files and folders each time you create a gallery.) Only the 'jbcore' folder should be integrated within the module.
As we did not write the module ourselves (and the problem you are encountering seems to be related to the gallery's embedding code which is generated by the module), you might also like to post in the Drupal forum where the author of the module should be able to help.
However, if you continue to experience difficulties, please post back with the URL to your gallery and I will certainly try to help further.