The problem with JProfiler is that, at times while drilling down it simply says "thatz the end of stack or so" (I couldn't recollect the exact message which was thrown).
I have observed this quite a few times. This doesn't happen in JProbe and I feel JProbe's result to be much more accurate.
Another difference is that, JProfiler can do on-demand profiling. JProbe is a little weaker in that. I believe, they have improved it in the very latest version. But till JProbe 6.0, it was slow, but its stable though.
If you would like to view the results from multiple perspectives go for JProbe (like object view, memory view, graph view, cumulative memory, cumulative time, average execution view and so on). Otherwise
you should be fine with JProfiler.
~Rajesh.B
