First, are you certain that the fuel pumps are providing the proper fuel pressure? Does the low fuel pressure indication occur all the time, or only at high throttle settings?
You didn't say which avionics you have, so I will assume Dynon and that by EM-221 you mean SV-EMS221.
On the RV12iS the displayed fuel pressure should be the difference between the pressure reported by the Kavlico fuel pressure sensor mounted on the back wall of the fuselage and the manifold pressure reported by the Rotax engine via the SV-EMS-221. So either of those two sensors or the wiring to the Kavlico could be faulty, or the sensor configuration in the EFIS could be wrong, or the fuel pressure regulator could be faulty.
If the issue can be seen on the ground, you can temporarily change the fuel pressure sensor type in the Dynon settings from the correct value "Kavlico 150psi DIFF" (assuming you have the Kavlico 150psi sensor) to "Kavlico 150psi" (without the DIFF). When the engine is not running and the fuel pumps are on, this should give you the correct reading (about 42psi) if the sensor and wiring are OK and you really do have the correct fuel pressure.
The flap position indicator is a totally separate system. You can go into the flap position calibration in the EFIS to see what voltage the position sensor in the flap motor assembly is reporting at various flap positions. Assuming the flaps deploy correctly, most likely you have a faulty position sensor in the flap motor assembly or an issue in the wiring between that assembly and the EFIS.
