In one of the recent ROMS updates for pre-version 3.0, the code now dumps an extra restart record if it gets in trouble. Upon restart, the code checks to see how many records are in the file. If it is more than two, it won't cycle between records one and two even with the cycle flag set to true. I'm getting mystery write errors probably due to some filesystem weirdness where things are fine on restart. However, if you don't do anything about it, the restart file is now going to grow uncontrolably. So here's the fix:
ncks -d time,4, nep4_rst.nc rest.nc
nep4_rst.nc is the old restart file containing five records and rest.nc will be the one-record new restart file. Remember that the NCO utilities count starting from zero. You also need to change the input file to point to rest.nc.