Discontinue using!

Until you find the source of the "short".  You could potentially damage your decoders.

Where do the units short out on the layout?  At frogs? crossings? or just randomly?  Frogs and crossings could be a simple as wheelsets out of gauge.  Either too wide or too narrow causing the wheel to bridge the gap at those areas.   If it's just randomly happening on straight track, then suspect a broken/chaffed wire some where along the electrical path from the trucks to the decoder.

So they were running for a while

Then the started to short out.  This could be electrical or mechanical.  Because they both seem to be doing it at the same point, it sounds like it is electrical.  The event that has created this condition happened to them both when in consist.

You need to identify where is issue is.  For that reason, you should take one of the units and work through the possibilities.

Make sure you have a record of the cv settings you changed with the program.

then I would follow a sequence like this:

1. reset the decoder to the default settings.  The run the engine on the layout.  Try to replicate as best you can your normal process, including sound activity.  If it starts to short out again, make a note about where in the process it happened.  

2. If it happened with one, then I would disconnect the sound unit.  The repeat the running.  

3. if it happened with 2, then take the decoder out of the unit.  You may have to rig up some contacts to be sure the DC connection is in place.

if it happens with three, then the  fault is with the motor.  If it happens with 2 and not 3, then the fault is with the decoder.  This last is what your description indicates, but with the costs involved, you need to be sure.

GP30s

The offending locos have been removed from the layout.  I had a four hour OPS session yesterday, and they worked fine at the start of the OPS session.  Then they began to stall, randomly on different parts of the layout.  About three hours into the OPS session they started shorting the layout, and the DCC system would shut down, but would come back on if the locos were moved.  Finally,the DCC system would not restart unless the locos were removed from the track.  All other locos  including other locos of this type continued to operate just fine.

I will do an internal inspection this afternoon.

I use JMRI Decoder Pro, so resetting CVs will be easy as they are saved in the JMRI software and can be sent to the decoder.

At this point I am suspecting a short in the wheels and I will pull them out and test them for shoring  against each other.

Sounds like a good place to start

let us know what you find.