I have to think this through - but one possibility is DCS signal interference from the FasTrack switches. This is a known issue, but examples solved so far have only been local areas and not the whole layout. It depends on your track configuration.
"Track is Fastrak and I have 4 power tracks in star config and proper polarity around a 7'x7' oval with an inner and outer turnout to allow me to run both trains at the same time." quoted from your post above.
The solution is to replace the track power jumper on the switch with a choke which filters the interference created by the switch electronics. You can order the choke from Digikey here
A method to test this is to remove the track power jumper from the switches and run the layout, power down and then power up the layout and determine if you still have communication with the engines.
edit: If they are manual switches this is not necessary, but if the turnouts join the two loops then see below.
Possiblility #2
A second problem that could exist is that you don't have the DCS signal blocks properly isolated. The length of a loop on a 7' x 7' table would only need two blocks per loop.
Two 5" Block tracks (Lionel 6-12060) would be needed or two 1 3/8" tracks at 180° apart with the center rail jumper wire removed to create two DCS signal blocks per loop. One terminal for the center rail would be used on each block track.
Using the terminal tracks creates power and signal input points, but does not create a power/signal block as there are no isolation points to separate them.
A quick test for this solution would be to disconnect all but one power/signal feed for the entire layout or one power/signal feed per loop if the loops have the center rail isolated.
Sketch your layout on paper and post a photo of the sketch.
We can help by showing you where you need isolation tracks to create the blocks. edit: this would really help to confirm the layout signal basics are proper
I believe that these two situations with the track and wiring configuration are a strong possibility of the source of the problem. The chokes for the switches are definitely needed and you may be affecting the signal by not having the block between the terminal tracks center rail isolated. A simple example is attached.