About your first issue. This is the A/T system protecting the aircraft during a dirt configuration (takeoff and approach)
-If you want to increase the speed, you need to retract the flaps as per the flap schedule, otherwise A/T will not allow speeding the aircraft beyond current flap setting capability not to rip the surfaces.
-If you want to decrease speed, you need to extend the flaps as per the schedule, otherwise A/T will not allow the aircraft to reduce speed below the minimal current flap maneuverability speed no to stall and crash.
note: make sure you do not use any hardware lever as an axis, unless you use a detent plugin or similar. Otherwise your potentiometers nois/spike will keep moving the flap position no matter you are not touching at them
About your second issue. Calculated VREF speed for landing is based on aircraft GW (Gross Weight) for the given flap options. If you are getting such a crazy low speed values, this would indicate you did not load anything on the aircraft during pre-flight.
Before departure:
1. Go to GROUD SERVICES menu
2. Select REFUEL TO xx tons of fuel as required for your trip
3. Adjust ZFW to around 50 tons or similar (this is pax + cargo)
4. press Instant to load everything.
This will result on an average packed aircraft and you will see what IXEG flight model is all about, you will actually feel the weight during TO pull and landing.
note: for the purpose of landing on calm days, you have to configure VREF +5 knots on the MCP SPEED DIAL during approach to cross the runway threshold at that speed and you bleed off those 5 knots during flare while you retard the throttles to a VREF touchdown.
Landing on windy conditions require more complex calculations to the VREF +XX, you can experiment later on this once you materized the above.
hope this heps