I have an issue where using the IMCE button in Ckeditor causes the popup to 404. I have tracked this down to the fact our Nginx configuration denies direct access to index.php for security reasons, and the popup path is explicitly "Drupal.settings.basePath + 'index.php?q=imce\x26app=ckeditor|sendto@ckeditor_setFile|&CKEditorFuncNum=' + editor._.filebrowserFnIMCE, width, height".
If I use the "Browse server" button through the "Image" dialog in ckeditor the path is correctly cleaned to /imce?app=ckeditor...etc.
I can't seem to find the js code that controls that browse server button but surely it's possible to clean the url in the same fashion through the imce plugin. Found out that this is controlled by a setting "filebrowserBrowseUrl" that's generated in ckeditor_profile_settings_compile[]. Could this not be used in the imce plugin.js as well? Also interested to see that the same plugin.js appears in the ckeditor library and the module for imce.
Support from Acquia helps fund testing for Drupal