Yeah, I too have had that problem. Check your axis handles and see if they are both pointing the the same direction. If not, that will surely be the problem. Theres a method for turning the axis handles so they point differently, but I forget how to do it at this time. Try freezing the transformations on both of the geometries as well. ( go to MODIFY / FREEZE TRANSFORMATIONS).
I'll inquire on how to turn the axis handles at school tomorrow.
Dave Baer
Professor of Digital Arts
Digital Media Arts College
Boca Raton, Florida
dbaer@dmac.edu