Things are much more stable now with rosetta, The new Apps 5.06 and 5.07 have built in abort for runaways, all CPU usage and points are reviewed and points granted on a weekly basis (fridays) for aborted units. :yippee:
v5.06 introduced a small bug in that the completion of the WU is controlled by how may nstructs the program runs instead of the total time. I did notice that some of the WUs I was proccessing ended earlier than my 8hr preference setting. The minor bug is fixed in the v5.07 WU that you proablay all have now unless your caches are quite large.
Read more here. You will need to take the grain of salt as there is a lot of froth in that thread.
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1499