I'm using JBuilder on PC at work (and Project Builder at home, of course) and the fact is, it doesn't use Aqua. It uses Swing, just made to look like Aqua. So all the hardware-optomised job of rendering those nice Aqua components is being done from scratch... in emulation.
I can't really think of any way around it, unless there's a better implementation of the Aqua theme for Swing - possible one that had native libraries to plug into the real Aqua rendering... which would make it OS X only, of course.
What Aqua theme are you using for it, anyway? Would it work on a PC?