I tried out consisting with 2 digitrax decoders with no problems with the switches.  I added a bachmann decoder in an F-Unit. this works fine also with the switches.  It doesn't appear to be any power limitations.

Are there different bachmann decoders in the SD40s then the F?
thanks for your comments

that's to bad about the sound. 

These are vanilla Bachmann SD-40s with the Bachmann chip. Nothing fancy.  and Bachmann HO #5 switches....   

I will test with a couple of Digitrax chips I have. 

I don't think so.  2 engines and 2 switches is the minimum I'm using to debug.

I understand the 9 function # to throw switches.  thanks.

I was testing out consisting when the problem occurs.  When I program the loco back to the original number all works fine again.  I've seen this with different loco combinations.

Has anyone seen this behavior?

I've programmed 2 #5 switches for a siding for remote activation.  Testing works fine.  However, when I run a loco, even momentarily the switches don't work.   
I press the stop button to flashing and again to solid and the switch flips.  I think may be cached.  Both switches work again until I run a loco.

Am I doing something wrong? or is there a bug in the software?