I tried to click regenerate in one specific file from the media listing and that worked. I mean, no file was created because the file was already 990px width, so i guess wordpress doesnt create another instance of it with "-990x600" in the end of the filename.
The script I use to show galleries, now shows the image with 990px though, instead of showing the file ending on "980x600", with 980px width (old "large size" in the media settings)
Maybe when you click regenerate on a single file it just overwrites the files even tho they are already there, and maybe that resets something and makes wordpress think twice about whats "large size".
I hope that makes a bit of sense. Is there a way I can make the Regenerate script behave in the same way that the single regenerate link works for each media file? And overwrite everything?