The problem with decomposed foam insulation affected early electronic sound boards, especially in steam locomotive tenders. I do not know if there are any recent uses of that insulation in more modern trains. Most electronic boards are now mounted with standoffs, or in plastic carriers.
The El-Capitan locomotive is an FT diesel. The parts diagram http://www.lionel.com/CustomerService/ReplacementParts/index.cfm?doAction=productPartFilter&number=6-24568&productID=f39c0a1b-3d88-4b90-8292-84d73496a6a2&CFID=55610727&CFTOKEN=470be726b056f309-E0266715-0D3A-8FA3-D29F963113C5F1D6&jsessionid=8430d78ed46d236187016226405944215262 does not show how the board is mounted, however.
Check all connections between boards, and between the boards and the chassis with any ground wires, if used. Also check all solder connections on all boards as stated above. If everything checks out, then a board may be at fault.

Larry