Please show us some source code. Maybe there is something obvious that we are missing. Do you use NEWT or something else? Which kind of animator do you use? Are you under Windows? Do you use the famous hack to force the use of the high precision timer (
ra4king already posted it in this forum)? Do you use the latest autobuild of JOGL 2.0? What is the version number of your driver?
Edit.: Maybe use vertical synchronisation and/or FPSAnimator. If it is still too slow, you will need some kind of (frustum, portal, contribution, ...) culling and spatial subdivisions.
Edit.2: It looks like you simply don't use the high precision timer. If I were you, I would just solve this problem and
enable vertical synchronisation.