MAAC,
Not confused, after running Mikes test, I believe you may find you wired one or more of your switches incorrectly, or the switch itself is not working correctly, giving you your problem, either that or you have a couple pieces of bad track in different places in your layout. Check every switch and individual piece of track in the areas where you are loosing signal, I bet you will now find your actual problem.
PCRR/Dave