I use PFPX for planning flights, and Flight Sim Commander for connecting with FSX, for route stuff, like time left, so i know where the AI is etc. I have a weird issue with the navigraph updates. PFPX will build a route, I export the route to FS commander, and when I open that flight plan up it tells me there are some waypoints that don't exist in the current cycle. However I've just discovered that if I copy that route, paste it, then it will let me save it in FSC. My question, is do I contact one or all of them, if only one, who do I contact? Oh and they are both using the same cycle.

If you bought PFPX, they have support.  Same with Flight Sim Commander.  

I would post on the PFPX forum. This is a problem with PFPX using routes that are outdated. There is a user who posts a fix every month when the navdata is updated, but not this month, due to xmas I suppose

Example http://forum.aerosoft.com/index.php?/files/file/2389-corrected-routes-airac-1312/