Institutionalization (gqtype in the CPS) is used as a proxy for incarceration in prisons and jails in some academic studies (i.e. Neal and Rick, 2014 http://www.nber.org/papers/w20283.pdf), however female incarceration has shown a remarkable increase over this time period. Any ideas as to why gqtype does not show this increase? It is possible that other types of institutionalization decreased enough to offset the change, but seems unlikely.
I actually think the GQTYPE variable used in this analysis comes from IPUMS USA, rather than IPUMS CPS. Indeed Table 2 in Neal and Rick (2014) cites IPUMS USA. It is a bit confusing, since the two variables share the same name, but they include different detail within their codes. In particular in IPUMS USA GQTYPE==1 identifies those who are institutionalized. I think if you use this variable you should recognize the trend you expect.
Sorry, I did actually use IPUMS-USA, but I incorrectly specified it as CPS (I meant to write ACS, I guess CPS was just on my mind).