It sounds like you have some issue with the lamp matrix wiring, a diode, etc. that is causing a problem. LED OCD can fix issues with timing and/or leaky transistors, but it cannot fix lamp matrix wiring problems.

Is there a pattern to what lights turn on and what lights cause them to? For example, anything in row 1 (11, 21, 31, etc) causes lamp 81 to be on as well.

You can use the "jumper and bulb" method to test your board outputs and narrow the problem to either a board or wiring issue. The Siegecraft lamp matrix tester is a great tool that makes this same test even easier. Neither of these test will pinpoint a problem in the wiring, though. The best way I know of doing that is to make a full summary of what lights you're trying to light and which acutually turn on, then look for patterns.

Incandescents require more current to light up than LEDs. If you have a small amount of current, the LED can light when the incandescent didn't. Also, while installing LEDs, you could have bumped something, causing a short that was not there when the incandescents were installed. When I say wiring, I'm using it to mean everything under the playfield vs the controlling circuits on the board.

It doesn't have to be on the lamp in question. You can have a shorted diode on a lamp that appears to be working fine, but it is allowing power to backfeed a different column. The full pattern will likely point to the issue. Diodes can leak, but in this case, it's unusual to cause what you're seeing. It's much more common for one to be squashed over and shorting to a socket.

There are ways to use the LED OCD to help diagnose, but you really have to know what you're doing, and usually it just complicates the diagnosis.