I'll address the title of your thread. The main installer, 2.3, comes with old style navdata. The new updates, currently 2.4.0.11, come with new style navdata (cycle 1013 is included, see ). The update does not remove the old style files, so there are indeed a bunch of them.
Just open one of the new style files, apts.txt for example, and you should see something along the lines of "AIRAC Cycle : 1101 (13/JAN/2011 - 09/FEB/2011) - Rev.2", just before the start of the actual data.
As for the rest, I think FS Build can take some getting used to, but it is one of the best flight planners for a reason and that is not a pretty but good for nothing GUI, of which there are plenty. Bottom line is, it works. If something doesn't, post here and Ernie will look into it, he offers some great support, IMHO.
