When I export a flight plan very often even with FSX, that RC4 would be empty where there should be way points in the window where there should be, there is no altitude information set either. Am I doing something wrong, does this just not work with PFPX?

PFPX does not add SIDs and STARs to created plans. Other than that I don't see why you should be getting a problem. There is an option to export in FS9 or FSX format and either should work with RC4.

 

Can you paste a plan here and I'll compare it mine using the same airports. Here's one I created for KLAX-KSEA. Ignore the unusual routing, it's for Concorde.

 

<?xml version="1.0" encoding="ISO-8859-1"?>

<SimBase.Document Type="AceXML" version="1,0">
    <Descr>AceXML Document</Descr>
    <FlightPlan.FlightPlan>
        <Title>KLAX to KSEA</Title>
        <FPType>IFR</FPType>
        <RouteType>HighAlt</RouteType>
        <CruisingAlt>35000</CruisingAlt>
        <DepartureID>KLAX</DepartureID>
        <DepartureLLA>N33° 56' 33.00",W118° 24' 29.06",128</DepartureLLA>
        <DestinationID>KSEA</DestinationID>
        <DestinationLLA>N47° 26' 59.60",W122° 18' 42.39",433</DestinationLLA>
        <Descr>KLAX to KSEA created by Professional Flight Planner X (http://www.flightsimsoft.com/pfpx)</Descr>
        <DeparturePosition>07R</DeparturePosition>
        <DepartureName>LOS ANGELES INTL</DepartureName>
        <DestinationName>SEATTLE-TACOMA INTL</DestinationName>
        <AppVersion>
            <AppVersionMajor>10</AppVersionMajor>
            <AppVersionBuild>61472</AppVersionBuild>
        </AppVersion>
        <ATCWaypoint id="KLAX">
            <ATCWaypointType>Airport</ATCWaypointType>
            <WorldPosition>N33° 56' 33.00",W118° 24' 29.06",+000128.00</WorldPosition>
            <ICAO>
                <ICAOIdent>KLAX</ICAOIdent>
            </ICAO>
        </ATCWaypoint>
        <ATCWaypoint id="RZS">
            <ATCWaypointType>VOR</ATCWaypointType>
            <WorldPosition>N34° 30' 34.30",W119° 46' 15.55",+000000.00</WorldPosition>
            <ICAO>
                <ICAORegion>K2</ICAORegion>
                <ICAOIdent>RZS</ICAOIdent>
            </ICAO>
        </ATCWaypoint>
        <ATCWaypoint id="DWORF">
            <ATCWaypointType>Intersection</ATCWaypointType>
            <WorldPosition>N34° 48' 31.74",W120° 39' 59.60",+000000.00</WorldPosition>
            <ICAO>
                <ICAORegion>K2</ICAORegion>
                <ICAOIdent>DWORF</ICAOIdent>
            </ICAO>
        </ATCWaypoint>
        <ATCWaypoint id="35N121W">
            <ATCWaypointType>Intersection</ATCWaypointType>
            <WorldPosition>N35° 10' 00.00",W121° 20' 00.00",+000000.00</WorldPosition>
            <ICAO>
                <ICAOIdent>35N121W</ICAOIdent>
            </ICAO>
        </ATCWaypoint>
        <ATCWaypoint id="CYPRS">
            <ATCWaypointType>Intersection</ATCWaypointType>
            <WorldPosition>N36° 25' 20.41",W122° 25' 55.85",+000000.00</WorldPosition>
            <ICAO>
                <ICAORegion>K2</ICAORegion>
                <ICAOIdent>CYPRS</ICAOIdent>
            </ICAO>
        </ATCWaypoint>
        <ATCWaypoint id="39N124W">
            <ATCWaypointType>Intersection</ATCWaypointType>
            <WorldPosition>N38° 40' 00.00",W124° 09' 59.99",+000000.00</WorldPosition>
            <ICAO>
                <ICAOIdent>39N124W</ICAOIdent>
            </ICAO>
        </ATCWaypoint>
        <ATCWaypoint id="42N126W">
            <ATCWaypointType>Intersection</ATCWaypointType>
            <WorldPosition>N41° 30' 00.00",W125° 30' 00.00",+000000.00</WorldPosition>
            <ICAO>
                <ICAOIdent>42N126W</ICAOIdent>
            </ICAO>
        </ATCWaypoint>
        <ATCWaypoint id="46N125W">
            <ATCWaypointType>Intersection</ATCWaypointType>
            <WorldPosition>N45° 30' 00.00",W125° 00' 00.00",+000000.00</WorldPosition>
            <ICAO>
                <ICAOIdent>46N125W</ICAOIdent>
            </ICAO>
        </ATCWaypoint>
        <ATCWaypoint id="OLM">
            <ATCWaypointType>VOR</ATCWaypointType>
            <WorldPosition>N46° 58' 17.89",W122° 54' 06.59",+000000.00</WorldPosition>
            <ICAO>
                <ICAORegion>K1</ICAORegion>
                <ICAOIdent>OLM</ICAOIdent>
            </ICAO>
        </ATCWaypoint>
        <ATCWaypoint id="KSEA">
            <ATCWaypointType>Airport</ATCWaypointType>
            <WorldPosition>N47° 26' 59.60",W122° 18' 42.39",+000433.00</WorldPosition>
            <ICAO>
                <ICAOIdent>KSEA</ICAOIdent>
            </ICAO>
        </ATCWaypoint>
    </FlightPlan.FlightPlan>
</SimBase.Document>

I actually figured it out on my own it was a matter of making sure things were set up right in the first place. Which Mine weren't.