O.K. I see what's going on here...  You have to set the frequency on the 2D pop up which is not reflective on the main panel as it should be (problem is on my system their both synchronized).  So what the heck is the NAV1 panel doing on the main panel in your sim that's different from mine?  Within the VC I'm also seeing the NAV1 settings synchronized with what I do with the 2D pop up (again are you using the FSX or the FS9 version.  It's a shame I can't tell from the screenshots)...  From the pics above I see '117.30' is still listed on the main panel even though NAV1 is tuned to '117.90' on the 2D pop up (what am I missing here)....

Are you able to call up the runway info on the lower ND screen when you  choose the landing runway within the FMC (you'll have to flip to the next page on the ND screen to see the route and what I'm talking about)?  :-?