Great topic! I agree with the basic premise that the SHAPE results are affected by numerous things besides the presence or absence of the three base pairings that the game's energy model acknowledges. Working to figure out those additional factors is perhaps the most cool aspect of EteRNA.
What tools did you use to create these images? Something other than RNA Composer to predict the 3D structure? And the renderings don't look like options I have seen in Chimera, though there could be plugins I don't know about. I'm especially interested in what you used to predict stacking interactions.