I have exactly the same issue with my rover and a Navio2. I have different sets of 3DR and clone 433MHz transceivers and they all interfere with the GPS. The older Hobbyking modules even affect the steering servo. It starts to twitch and pulse as soon as I plug the module into the USB port. If I use a cord and move the module around, the twitching varies in strength.
I use those modules without a problem in my pixhawk controlled copter and a pixfalcon controlled Twinstar. The copter has a Ublox 6 GPS and the Twinstar the M8N GNSS that came with the pixfalcon.
i have a cheap 3dr clone 433, i did not notice a big difference on Navio’s gps, but I did not get any sats when using a similar 3DR clone 433 on an old APM2.8 with a neo7m when placing antenna really near to the gps;
i will test that on the weekend;
if i had those problems i would solder some capacitors to the 3dr GND/5V+ and observe if the (high frequency) power peaks from the 3DR modem irritate the ublox gps chip from the rpi usb power lines; (because @schuermannsebastian says they work fine on his pixhawk)
otherwise just distance between 3DR and GPS or maybe shielding would help…
The weird thing is that if i attach the RF after having got a fix, and then restart ArduPilot I’m able to get GPS fix, but then my accel/gyros become unstable (unstable horizon)
I tried covering the RF module in aluminium foil which stops the interference from being audible in my speakers, but still if I power on the RPi with the RF module attached I get no GPS Fix.
If I power on with the RF module physically detached, start APM and wait for GPS Fix and then stop APM, attach the RF module and start APM I am then able to get a GPS Fix??