LNAV HDG not following flight plan

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jerel2k4:
After I engage the FMS which indeed is working because I see the VORs, NDBs, etc displayed in the PFD and MFD descending distance as I fly.  I engage the NAV button.  So I have NAV, HDG, ALT, BNK, YD and FD1 lit on my autopilot section.  It shows LNAV HDG <--- ALT or TO.  It is definitely TO when I engage the TOGA on the throttle prior to departure.  <I HOPE IM EXPLAINING THIS CORRECTLY>  When I engage NAV the LINE showing between the waypoints on the MFD is still magenta.  Same color when I engage FMS.  According to the manual the line should be white.  Is this why the autopilot is not following the flightplan flightpath.  The reason I am asking is because sometimes when my plane appears to be within the flightpath, RADAR CONTACT says I am deviating my flightplan or flightpath.  I want to make sure I am following protocol in use of the autopilot before I start bellyaching at the RADAR CONTACT forum.

Thanks in advance!

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