On our multisite server I found Builder Style Manager from iThemes had a java script error with the domain mapping. It was seeing the ms domain name and the mapped domain name and getting confused.
On the same sub site today the new NextGen for MS would allow me to pick images but the upload failed. I removed the domain mapping and the problem went away.
FYI I had no other plugins enabled.
I'd be happy to help troubleshoot, I know there are a lot of NextGen users out there maybe not as many Builder Style Manager?