That rumor is completely false
JBuilder is one of the easiest IDE's to use, and I find it's pretty configurable as well.
I've never had it use it's "own" classes.. unless you're speaking of GUI building, in which case, yes, the wizards will use some Borland classes, but no one is forcing you to use wizards. All IDE's are guilty of this, to some extent, particularly for GUI building.
That said, we've built AWT and Swing applications using only classes found in jdk1.1.8 and jdk1.3 respectively.
JBuilder is also a 'clean' IDE because it doesn't stomp on any system classpaths. (take notes webgain)