The PC that is working properly is running Windows 7 and Sketchup 8. The materials libraries in the new (old) PC are showing up in Kerkythea. I was going to remove both Sketchup and Kerkythea and then reinstall, but for some reason Kerkythea is not even showing up when I try to add/remove programs.

In general the alignment will require a translation and two rotations. You have speciacl case with the way the two axies are aligned ( and their circular symmetry) and where the components axis are place . Slelect the short tube start move and type [0,0,0]. That will move it to the 0,0,0 global axis location installed as Dave shows shows above