SF340 First Officer experiences POS UNCERTAIN message on FMS during arrival. A clearance direct to a waypoint results in aircraft turning the wrong way. Vectors are provided to a normal landing.

Narrative

Enroute to destination message flag occurred on FMS. Message stated POS UNCERTAIN. ATC started giving heading vectors before problem needed to be solved. After several heading vectors from ATC; they gave us direct to an enroute waypoint. It was input into the FMS by the PNF and verified by PF. No message flags were shown on the FMS at that time. When initiated the auto pilot turned the aircraft to the right; opposite the direction of the waypoint. According to the FMS that was in fact the direction to the waypoint. As the crew was confirming this with other navigational sources ATC gave us a heading back towards the airport. Remainder of flight was continued without incident. The FMS location was not correct. Our situational awareness was slightly off due to the repeated vector turns from ATC as we were in IMC. We were about to question ATC about a vector when they offered one on their own. The FMS was written up upon landing for both the POS uncertain and the incorrect positioning during the flight.