NEED HELP.! Mainline Crossing

Do you have a break in the outside rail at both ends of the crossing? The outside rail must be totally isolated or the crossing wont work. ALL of the metal ground straps must be removed from the track that is between the 2 breaks in the rail. If there are any straps in place or there is only 1 isolation break, the gates will stay down and the crossing wont operate correctly..

Like Jathawk500 said, the issue is the insulated(isolated)rail is not isolated for some reason. A simple test is to have the power off and test continuity (ohms symbol - infinity) with the meter , of the isolated rail to any other rail. There should be none - 0 - no movement of the needle.

Check each side of the cut in the rail to ensure the cut is wide enough - then check that all bars are removed on the trigger track area - 

Page 6 of the manual for 6-14098 has the wiring diagram

Thanks, please stay with me on this, I've done exactly what you have said but will take pictures and check wiring one more time. 

All ground straps removed, made sure that I isolated both sides of OUTSIDE rail that the yellow wires are attached to. Question: JUST Making sure, the Center rail and Inside rail are still connected to the rest of the track? Sorry this seems so easy and yet has caused a lot of time trying to figure this out. Again I have a ATLAS transformer that runs to a circuit board, both leads, RED and BLACK are attached to that... connecting them to the crossings. I have a Brick that runs to a MTH DCS that goes to another circuit board that controls the power to the track. I phased both circuit board together. WHAT AM I DOING WRONG? 

The crossing gates stay down and blinking .... I tried just a truck and the crossing gates work sometimes, I try the train and the train gets shorted out before the actual break/isolated track... TOTALLY CONFUSED!!  

I cannot find a photo of the terminals on the bottom of the flashers - but, as a guess, the yellow wire and the red wire terminals should be switched as you have a power constantly on condition.

Here is an old thread that handled the same issue

Thread 1

Another thought - from your 8/25 reply - "I phased both circuit board together." 

You can do the phasing at transformers if they are close together - this means connecting the common or U or black wires only.

How to phase transformers video

I still think that you are feeding power to the isolated rail somehow - a wiring check is in order

Outside insulated rail activation video

Thanks, I will go thru the system again