Would you mind posting the .SCAD file so we can take a look? But... Even if you can't do that I have a couple of thoughts. Can you turn the matrix of cylinders into square pegs? The reason is spheres and cylinders have way way more triangles to 'compose' them than flat surfaces. Almost for sure that will make it render faster and use much less memory.

I have switched to the 2015-03 version of OpenScad. It is better than the previous version. But I have managed to get those same pop up windows. And once you get OpenScad sick, I think it is best to shut it down and re-open it. It appears to work if you don't do that. But it seems like once it gets sick, it never recovers. There is a very active OpenScad forum. I suspect if you post the code that blows it up a fix will happen!