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I have the same problem, but I have found a trivial workaround that works in 6.4.1. I generate two 3D plots and I want to be able to manipulate them interactively, side by side. However, as you experienced, I saw only the second plot. My workaround still doesn't let you have the plots side by side horizontally, but they are side by side vertically. In my notebook worksheet I generate both 3D graphics objects in cell_1, but then, I apply show() on one of them in cell_2 and the other one in cell_3. I have then two interactive Jmol 3D plots right on top of each other and I can interactively manipulate them separately.

Of course, I can also export the plots as Jmol scripts (using the right-click Jmol menu) and then use the standalone Jmol program to show them side by side in two different Jmol windows.

Hope this helps,