There's a bug in output.F in ROMS 2.1 that breaks handling of averages files (and I think diagnostic files) in this case. The problem is that at each restart a new averages file is created, overwriting the previously existing one that had the data. (This is hard to explain here. I can give a detailed example if necessary. Or try it for yourself.)
The cure is to change line 110 of output.F, ie
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IF (idefavg(ng).lt.0) idefavg(ng)=ntstart-1
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IF (idefavg(ng).lt.0) idefavg(ng)=ntstart+navg(ng)-1
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ifile=(iic(ng)-1)/ndefavg(ng)+1
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ifile=(iic(ng)-navg(ng)-1)/ndefavg(ng)+1
This bug has been reported and fixed before, but seems to have crept back in. I have been told that there are people who prefer the ROMS 2.1 behaviour and don't like my "fixes". If so, please speak uyp.