Hello. Same problem here.
I try to watermark images that will show in Envira galleries.
It seems IW apply the watermark to many image sizes but not to the sizes Envira is using. Using FTP I see about 15 sizes per image. It seems that those used by Envira have a _c ending.
Example:
Croco-Dior-granada.jpg (original full size)
Croco-Dior-granada-150×150.jpg (thumb, IW seems to work)
Croco-Dior-granada-640x640_c.jpg (Envira size, IW not working)
Thanks for your help!