When I run my application with -XX:MaxJavaStackTraceDepth=-1 the profiler doesn't print any stack trace. The output consists of the following.
--- Execution profile ---
>Total samples: 38441
>Non-Java: 3681 (9.58%)
>GC active: 490 (1.27%)
>Unknown (native): 21475 (55.86%)
>Not walkable (native): 9409 (24.48%)
>Unknown (Java): 838 (2.18%)
>Not walkable (Java): 2533 (6.59%)
>Deopt: 15 (0.04%)
>
>Frame buffer usage: 0%
Removing the option solves the problem. If it's expected behavior, it'd be great to document it in README.