Communications and GPS must either both or neither be present
First off, you imply that you want communication satellites to be possible, but not GPS satellites. This is simply impossible. Communications satellites and their ground stations depend on GPS in order to operate. A ground station must know its exact GPS coordinates in order to meet its timing windows for communicating with a satellite using TDMA, for example. If the ground station is moving, then it has to recompute its distance to the satellite on the fly, every time it moves. The satellite itself is also probably moving, most satellites have some sort of orbital precession. When windows are miliseconds wide, a few hundred kilometers can cause you to miss your window (at the speed of light, 1 ms is worth 300 km, for example)
So, if you have communications satellites, you also have the ability to make some sort of navigation system, and the requirement to have some sort of navigation system in order to allow those satellites to work.
There are several links in the GPS 'chain' that could be broken to prevent GPS (and communications).
How to prevent satellites
This could be accomplished by Kessler Syndrome. Lots of orbital objects can cause cascading failures that all but ensure that anything put into orbit will be hit by particles at tens of kilometers per second. If your planet were colonized at one time, then there was some Kessler Syndrome catastrophe, then it would become cut off from the outside world.
Removing satellites doesn't prevent older electronic navigation systems such as Loran-C. However, it takes time to set up that sort of station. If the colony is young, or doesn't take up that much of the planet, and if the Kessler catastrophe is recent, then perhaps navigation stations haven't been set up over much of the planet. If you find yourself on the far side of the planet, for whatever reason, there is limited radio communication on HF bandwidths (which is not good quality signal) and potentially no navigation beacons.
Preventing all radio signals
In this situation, an atmospheric radiation event has occurred that is causing significant interference. The GPS signal is not powerful, around -160 dbW. This corresponds signal is in the femtowatt range; not much at all! For comparison, this is about three orders of magnitude less than the minimum wireless signal your computer or cell phone can pick up.
All it takes to disrupt this is EM noise at the appropriate frequencies. You can invent some sort of stellar and/or atmospheric phenomenon that is operating at the appropriate frequencies. To prevent existing satellites from being quickly repurposed to alternate frequencies, the noise will have to have a pretty wide band. Fortunately, stellar phenomenal can be pretty wide band...like all bands if your star suddenly starts some kind of radio emission (for details on that...ask a different question!). Given that the wireless in your house isn't killing you with radation (we hope) this stellar interference wouldn't have too much affect on the biology of the planet's surface.
In any case, in this scenario, after colonization of the planet (since who would colonize a planet where radio doesn't work) the star started a period of unusual and unpredictable stellar activity. The planet's magnetic field is protecting the biology of the planet from the unusual radiation activity, but radio spectrum interference makes satellite navigation un-workable. As the planet rebuilds communications capacity with higher power transmitters to cut through the noise, there could be a time gap of decades where communication and navigation is limited. Alternately, the magnitude of the radio interference makes higher power infeasible, rendering communications moot until the star changes its mind.