I'm surprised they didn't specifically seek out a receiver that implemented the rule correctly. Since it's an "and", not an "or", a proper receiver should have kicked back in by the time it reached apogee.
I worked at one of the major GPS manufacturers as a hardware/firmware designer and we stopped tracking above a certain altitude and over a certain velocity due to government policy.
I remember one time there was a bug report from a customer complaining that our GPS would not work after mach 2 or some extreme speed. This ended up being a "qualified" foreign government client, so a new firmware version was sent which removed the restriction.
It says here[1] "All GPS receivers capable of functioning above 18 kilometres (11 mi) altitude and 515 metres per second (1,001 kn)[56] are classified as munitions (weapons) for which U.S. State Department export licenses are required. These limits attempt to prevent use of a receiver in a ballistic missile." News to me!
But the rules is that the gps devices needs to record a measurement greater than 100k feet. If that's higher than what GPS satellites can see then no one can win.
First, GPS satellites are in orbit ~20,000 km altitude, so this rocket is nowhere near too high. The beamwidth is pretty wide (it covers the entire half of the Earth, after all). Some quick research shows that below 3–4000km, there isn't much difference. http://emergentspace.com/gps_pubs/SSVP-v1.07-2column.pdf.
You should be able to get exact orbits (to the centimeter!) from the NGS (http://www.ngs.noaa.gov/orbits/), if you're interested.
Second, its the receiver that sees the GPS satellites, not the other way around. The satellites transmit, the receiver does not.
Perhaps the GPS devices were disabled by speed, or altitude, and didn't have time to reset while at apogee to get the reading.