John,
What you are experiencing comes from using 2 different generations of FasTrack. I have been warning people about this for quite some time, your early generation FasTrack was made with very serious quality control, your newer FasTrack unfortunately was not. The difference in rail height often happens with the newer FT. To counter act this screw everything down and tap the rails even, at every matching join.
Use all your older stuff 1st, then transition into your newer track, do not mix the Older and newer FT as you build, if you can, use a short piece of 3" 1st Generation FT to transition into the newer stuff. Work the pieces together properly for a good fit.
The very best thing you can do is try to acquire the 1st or 2nd generation FasTrack at your local Trains shows, the black mid-rail FasTrack was the very best FT ever made, pick up as much of it as you can, the 2nd generation track was almost as good, unfortunately identifying it can be a problem for guys just starting to use FasTrack.
Now the problem with the later generation FasTrack is actually the rail height, it varies all over the place, and if you use it, you must fit the rail heights together by tapping the track joins evenly and then each piece of track must be screwed down so it will not move. For Carpet Centrals us the clips and the zip ties for best results. Take the time to drill the holes properly in every piece of Carpet Central FT. It works pretty decently using this method. However FT works best when screwed down.
I am very careful when purchasing FastTrack.
PCRR/Dave
99% of everything you see in my Train Room is 1st and 2nd Generation FasTrack. It runs smooth as glass. Both on the Ceiling Shelf Layout, the Bar Top loops, and the lower platform, the numerous FTCC Switches are incredible engineering, and work perfectly from my Legacy Cab2 HHRC.
The RealTrax Formal Living Room Christmas Layout is screwed down in the same manner, running on a 3/4 Ply Wood Base on 2X6's. It also runs incredibly smooth, like the Train Room FasTrack.