I’m currently starting with WP and while using the NextGen Gallery, I stumbled over the same problem. Thought it would be fixed with 1.4.0 but nada, still the same problem.
So, setting a number of specific columns brought me to the idea that this maybe could be done per page with custom fields. Although it is not mentioned, I just tried ngg_gal_Columns for a specific page, and it worked. At least for me (and for the moment) this is a solution I can live with ??
Thought this might be helpful for others.
Cheers,
Wyando
