Below are a few suggestions...

1] Clean the End Of Stroke (EOS) contacts on the coil switches and the cabinet flipper switches.

http://www.pinballlife.com/index.php?p=product&id=995
https://pinside.com/pinball/forum/topic/vids-guide-to-upgradingrebuilding-flippers

2] Optimize the flipper adjustments in the LOTR software (V8.0 and higher).

http://www.sternpinball.com/upload/downloads/sb151.pdf

3] In your photos, I don't see a capacitor attached to the cabinet flipper switches? Mine have ceramic disc capacitors attached, but I'm not sure if they were installed at the factory, or installed later by one of the previous owners? I understand the purpose of the capacitor is to reduce arcing and pitting on the switch contacts. See the links below for a similar setup on The Sopranos.

http://www.marcospecialties.com/pinball-parts/500-6889-01
http://www.sternpinball.com/upload/downloads/sb156.pdf

I'm not sure if #3 above is a potential cause of your problem, but I thought I should mention it, just in case. Perhaps it will prompt someone else with more information to chime in?

Hope this helps. Good luck with your troubleshooting. Keep us posted on your progress.