I'm no CALIS expert, but I think you either have to accept that 12 rows wouldn't be part of the analysis, or try to clean up you source data. This quote from on-line doc might give some clues as well:
Missing Values
If the DATA= data set contains raw data (rather than a covariance or correlation matrix), observations with missing values for any variables in the analysis are omitted from the computations. If a covariance or correlation matrix is read, missing values are allowed as long as every pair of variables has at least one nonmissing value.
Regards,
Linus
Data never sleeps