Ok did another test and looked at the logs, nothing to see unfortunately.
It did mange to run a few iterations of latency before going bang:
root@beaglebone:/usr/xenomai/bin# date;./latency
Fri Dec 2 10:48:36 UTC 2016
== Sampling period: 1000 us
== Test mode: periodic user-mode task
== All results in microseconds
warming up...
RTT| 00:00:01 (periodic user-mode task, 1000 us period, priority 99)
RTH|----lat min|----lat avg|----lat max|-overrun|---msw|---lat best|--lat worst
RTD| 34.374| 317.362| 801.291| 0| 0| 34.374| 801.291
RTD| 29.291| 295.369| 481.624| 0| 0| 29.291| 801.291
Not very good figures!