It's possible that a formatting error has been introduced in the env xml files. If there appear to be problems with the env variables (i.e. if the model doesn't seem to have consistent values compared to what's set in the xml files), then confirm that the env variables are being set properly. There are a couple of ways to do that. First, run the ccsm_getenv script via
> cd $CASEROOT > source ./Tools/ccsm_getenv > env
and review the output generated by the command "env". The env variables should match the xml settings. Another option is to edit the $CASEROOT/Tools/ccsm_getenv script and comment out the line "rm $i:r". That should leave the shell env files around, and they can then be reviewed. The latter approach should be undone as soon as possible to avoid problems running ccsm_getenv later.