I have exactly the same problem with newest version of WP and Nextgen 2.0.65. I was switching plugins to on and off and I see that conflict may be with mqTranslate and or Advanced Custom Fields. But mainly please focus on mqTranslate (for of dead qTranslate).
I use as an effect thickbox. I save. Then it is removed from the select / option. I choose another effect and again the same result. Can you fix this?