I'm a little confused as to where you have placed the isolating sections. If I am reading things correctly, you state that you have placed them either side of each switch. This will not work, and you'll have a completely dead crossover. The isolating sections should only be placed between the switches in the spaces between your two tracks. This is to keep each track electrically independent of the other.
If however, you have done this, and the problem only occurs when a train tries to use the crossover, then it most likely is a matter of phasing as suggested previously.
Would you please be kind enough to let us know some more detail as to how you have wired your layout in order for us to help further?