Continuing the discussion from Trying to run the Fiji:
I doubt these problems are specific to El Capitan. It is possible, but there have been drag-and-drop-related issues in the past. This issue is likely to be similar. Does drag-and-drop for other microscopy file formats work? (Specifically: formats that require the Bio-Formats plugin to open.) And what about standard formats like PNG and JPEG? Do those work with drag-and-drop?
As for the LEI behavior issues, do you have the same problems if you use File Open… to open the LEI? Or does that bring up the Bio-Formats Importer Options dialog as expected?