This issue was discussed on the mailing list (8 October 2010 21:55:08 GMT+02:00) but never made it into a bug report. I have reproduced the problem on Damiana and Queen Bee. If I submit a simulation and let it run and make some checkpoint files, and then submit the same simulation again, a second restart is correctly created, but I get the warning on startup
WARNING[L3,P0] (IOUtil): No HDF5 checkpoint files with basefilename 'checkpoint.chkpt' found in recovery directory .
and the simulation starts from iteration 0 rather than recovering.
It looks like simfactory is not hardlinking the checkpoint files from the old restart to the new restart. Being able to use checkpoint/recovery is absolutely necessary for production work.