Not sure what to call this problem, so the title is probably incorrect. Here is the issue I have been experiencing for awhile. Every time I try to build a flight plan I start with the usual, departure, destination, Sid, and then STAR. I then start adding JET ways, for example CTY J91 ATL and so forth, but once I have to insert VOR, NDB, or INT FSBuild installs it at the beginning of the flight plan, just after the departing airport. I have been experiencing this issue prior to the update and even after the update. I have also did a fresh install as well and still this issue.
Running Window 7 Pro
It isn't clear what's going on here; I have never seen the behavior you mention... CTY and ATL are VORs - if you omit the airway do they remain where you put them? Can you provide a step by step example of one of your routes?
One thing you should do is limit the search radius that FSB uses to locate nav points - go into Options|Settings and set the "Autogen Route Combo Limit" to between 100 - 300.