I reported a JDI problem using the bug report page but had it rejected because of not providing a test case. This is annoying - a test case is not always practical, and in this case it should be obvious that it is not, and that the problem is serious enough to at least notify an appropriate developer. The bug report reviewers should be allowed to user their common sense.
Anyway, with build 1.6.0-ea-b47, ThreadReference.isAtBreakpoint() and ThreadReference.ownedMonitors() are sometimes very slow, taking as much as half a second to complete. This is not always the case, but seems to happen immediately after a breakpoint event, for example. We always call these while the vm is suspended. The problem did not happen in Java 1.5 or any previous versions. Our debugger continuously displays the status and monitors for each thread, and because of this it is basically unusable under Java 1.6 (for now, we have disabled those features when running under 1.6 ea, and there don't seem to be any other problems).