Do you have regular incandescent bulbs installed in the game, or LED lamps?

First... LED or Bulbs?

If LED, go to Adjustements / Standard Adjustements / Allow Dim Illumination - set this to off.

The 'bulb saver' technology that WPC machines use is really remarkable, but they dim the incandescent bulbs by shutting off power to them. LED's have a really obvious flicker effect... unless you buy the higher cost 'flicker free' LED bulb replacement from Cointaker.

The bulb saver technology uses some circuitry called 'zero cutoff' and I've always suspected that problems with the 'zero cutoff' section could cause inappropriate flickering, but I personally haven't seen this problem.

All your (controlled) lamps use the +18V, so a problem with a fuse acting like a resistor at F114, browned pins/plugs at J101 could starve the 18V of it's power. BR1 is the bottom Bridge Rectifier under the big silver heat sink, and a failure here could mess with your 18V. An absolutely failed C6 and C7 could cause you to not have smooth DC voltage, but I've replaced a crazy amount of failed bridge rectifiers and VERY few 15,000 uf capacitors.

Troubleshooting.

You did the right thing. The General Illumination and the 'controlled' illumination are different. Isolating the problem to only the controlled illumination side helps.

LED's and Dim Illumination setting are what happens when you are not playing... like fifteen minutes after you stop playing (adjustable) the lights would dim down by flickering.

In test mode / All Lamps, do the lamps come on brightly without flickering?

I would re-seat J101 on the right side of the big Power Driver board. I'd visually inspect the capacitors for leakage, and F114 for any indication that the fuse has been getting hot.

I'd re-seat all the grey ribbon cables (with power off).

Then (with power back on) I'd use a meter to find out if my +18V is reading correctly.

After that, I'd be looking deeper at the lamp and the zero cross circuitry.

Let us know what you find!

The recently released L8.3 update also includes a fix for the GI Power saver:

A.2 25 Lamp Driver
Added in L8.3 and selects the lamp matrix update code the game will use.

Original: The original L-8 lamp matrix code is used unaltered.
LED: The lamp driver uses updated code to prevent ghosting. This update is intended to prevent LEDs from flickering. This includes extra fix to prevent a ghosting that can take place when game goes into "GI power saver" mode*.

*Note
The game supports a feature called "GI Power Saver" through adjustment A.1 29 and A.1 30 which is used to reduce the general illumination brightness. Although this mode is named with "GI" it also happens to be that the non-GI lamp matrix code also has a slightly different behavior during the "GI Power Saver" mode, inserting a small pause after the 8th column has been updated. The "LED" setting updates the lamp driver to prevent ghosting that can take place during this small pause.
The A.2 25 setting is only related to the lamp matrix code and does not affect the code related to the general illumination. LEDs used in the general illumination may still flicker during the GI power saver mode, regardless of the setting of A.2 25.
In connection with the setting for general illumination brightness, the recommendation for A.1 25 using LED is No.

With power off, press on the square U9 ASIC chip on the MPU board and then reseat the short ribbon cable between the MPU and Driver board on both sides of the ribbon cable.

Did you put another driver board in T2 to be sure it cleared up?

I never seen a driver board act this way, but I could imagine C2 could have leaked and damaged traces below it affecting the blanking signal.

Could you post a picture of that driver board?

T2 and Gilligan's island both use the same -1 driver board which has the relay section populated in the top left section of the board.

Let's see the board. I would put GI board in T2 to verify and you know it is a good board, which I would leave it in T2.