Linking prims throws off rotation?

Right now I have a bunch of prims that when I link them together as an object always take the rotation and axes of one of the child prims rather than taking that of the root/parent prim. How do I keep this from happening? I select the properly-positioned root prim last every time when linking it and as soon as everything's linked the rotation and axes inevitably are set to that of the differently-positioned child.

This is a long-standing bug that only affects some people in SL. No one has ever been able to figure out why it happens to some people and not others. It's downright bizarre. It was actually fixed for a short time, but then resurfaced a few weeks later. Again, no one knows why.

Anyway, what happens is the linkset takes it's rotational values from the second-to-last selected prim before linking instead of from the root. The only way to combat the problem is to work around it. Give at least one other prim the same rotation as the root, and make sure to select that one second to last before you link everything to the root. That's really all you can do.

I just tried the method you described but it still has the problem, you link everything and it shows the right location but as soon as you select the linked object again it shows the wrong rotation of the child prim.

Just for fun try putting the rotation script into a prim at the center of the build before linking.