I am also having problems getting the JavaScript debugger to stop on a breakpoint. I downloaded the JavaScript QuickStart (Mario). That worked okay. I was able to stop at a breakpoint.
I then created another MyEclipse J2EE Development project and tried to debug that code. The debugger did not stop at the breakpoints. I inserted a JS alert() statement before my breakpoint and they popup, so I am definitely am running the application where I should hit a breakpoint.
I then terminated my application and tried to debug Mario. That also failed to stop on a breakpoint, so whatever I did also broke the debugger. I tried closing the J2EE perspective and the debug perspective and restarting, but that made no difference. I then terminated all of MyEclipse and restarted it.
After restarting the workbench, I was again able to debug Mario, but the first time I try to debug my (very simple) JavaScript, it fails to stop on a breakpoint on either my application or on Mario.
I can recreate this on demand.
I am running:
MyEclipse v5.0.1GA (20060810-5.0.1-GA)
Windows XP SP2