I'm using Navilock NL-552ETTL Ublox5 GPS module with the latest firmware.
And I mount it direct over the AP board on the additional copper layered
plate. I've played with the distance between them, mount direction - it
also makes difference. However the problem is not completely away. Now I
incline to use an additional AP board covering.
Yes, I'm using libopencm3, I've forked it to my repo (
https://github.com/softsr/libopencm3 ) and currently working there.
I'm using a Paparazzi master branch, however I didn't track it for a long
time, so I'm going to do it yet to be synchronized with the current master
version.