I’ve used this plug-in with images in a NextGEN Gallaery and it works just fine. NextGEN doesn’t change the way the files are stored in the media library so there’s no issue at all.
The plugin can search for 250 images that meet the resize criteria at a time and convert those results with 1 click. So if you want to resize over 6,000 images it will have to be done in multiple batches.
I tried setting everything as 777 but that just breaks a lot more than it fixes. Is there a list somewhere of exactly what files need what permissions? I went through the troubleshoot guide but none of related to file permissions.
And I just figured it out, just set the cookie timers to 1 second 🙂