sd60 proto 3 starts sporadically

Remove the connectors so the wires are free.  Bend the capacitors over so they lie horizontal over the board, vice up.  Lay wires over the capacitors and replug the connectors in.  Test.  G

If GGG's advice doesn't solve issue, I'd contact MTH in Columbia MD before the warranty expires.  Be careful with that 40-pin connector--the wires have a reputation for fragility.

Thankyou GGG! I'm pretty sure I did what you said correctly. Since your advice, and my tinkering, I've tested it 30 plus times, last night and throughout the day today, and she has started right up! I still do not quite understand what unplugging the wires, bending the capacitors horizontal, and re connecting do? But I do know it has started more consecutive times in the pass 20 hours then since I've owned it. Again I appreciate your time and knowledge.

When wires run across top of circuit board and near the signal transformer they can degrade DCS signal, even to the point of effecting other engines on layout.  Having the wires above the caps reduces that interference.  Your welcome.  G.