Assuming nothing is wrong with the new boards, you might have bad female connectors. My Gorgar was having horrendous switch issues, and it turned out to be bent connectors on the female end of the plugs not making good contact. I'm not familiar with the design of the rottendog replacement, so I couldn't tell you off hand which connectors go to the switch strobe/columns, but It'll probably the 2 connectors on the right hand side of the board. Pull them out to see if they're bent or corroded. Note: Reseating connectors really won't do much at all.

It couldn't hurt to repin those connectors anyway, as that'll be cheap bulletproofing insurance. If fixing those connectors doesn't work, you might have a board problem.

I would say that this is almost certainly the case. Molex connectors only have a connection life span of about 20 (at or about) connects and disconnects (+/- a few), and being that the game is already 30+ years old, it has most certainly exceeded that lifespan. Metal corrodes, and the elasticity of the pins wears away over time. Repin those female connectors. If the problem persists, you have a board problem and should contact rottendog.

I recommend the molex .156 trifurcon pins. Those are the best.

It's honestly a really simple job, and there's very little room for error. Grab yourself a pin extraction tool, a crimper (you'll need to get a proper molex crimper) and a handful of those molex pins. I recommend Great Plains Electronics, but it looks like a lot of their pins are out of stock. I tend to order from Mouser Electronics mostly anyway as they stock more stuff.

Give this tutorial guide a good read. It should answer most, if not all of the questions you might have: http://www.pinrepair.com/connect/

Good Luck!!