Due to NextGen's current direction for their plugin, I have moved to using NextCellent. Unfortunately, WP Supersized doesn't quite support using NextCellent. I think it can pick the folder that NextCellent uses, but only when editing the general settings, not page specific.
After an hour or so, I have come up with a solution which appears to work. For those who want NextCellent to work just like how NextGen worked, you can get the code off of github here. github.com/recognizerHD/wp-supersized
It's been forked from the 3.1.6 code and the only changes (as you can see) are for the NextCellent support.
Hopefully this gets rolled into the next update, whenever that is.