The first thing to note is that COUNTY is not currently available for 2012 data files due to the change in PUMA codes and boundaries (detailed in the release note for the 2012 data files).
Counties are not actually made available in the Census Data after 1950, but IPUMS-USA used the smallest available geographic unit to construct counties. More details on this construction are available in the COUNTY variable description as well as a downloadable excel file listing the counties that were identifiable in each sample. Respondents who lived in the counties that are not identifiable (if component boundaries extended into other counties) were given a code of ‘0’. The lack of a county code does not necessarily imply that the county was not sampled, just that the component geographic units do not perfectly match up with the county boundaries.
I hope this helps.