I'm using the theme rt-theme 17 (themeforest). The theme itself has a function by clicking the portfolio-featured image it opens in a new window.
If there is a nextgen-gallery in the same article, then a click on the featured image of the article opens two windows on two layers. After clicking on the second picture (I think from nextgen) this will close and the right image of the theme-function is viewable.
This problem don't exist with the nextgen version before 2.0. Hopefully this will be fixed. It should work in the same way than before with 1.9.13.