If you are using JDK 1.6.0_14 to develop, upgrade to JDK 1.6.0_16 - it was released to fix this single bug. (you also as a benefit get 1.6.0_15's security updates)
This caused me some headaches, as it didn't always miss my breakpoints in the debugger, only occasionally... I didn't realize the core problem until a coworker informed me.
Here's a link to the bug:
Release notes for 1.6.0_16:
Download links to the JDK are somewhat cryptic looking, but here goes:
If that fails for any reason, just go to java.sun.com, click on Java SE on the right, and there should be a JDK 1.6.0_16 (non EE) link on the page.