As per some of the suggestions floating around the forums, here's what I've been doing with my boards:

Spray the board with simple green, let it sit for a few moments, and then attack the problem areas with a soft toothbrush (if any finish or traces start flaking off, then stop--this probably isn't an ideal approach for this board). Then, run the board under warm water to rinse it off. Rub on some 91% alcohol (this should displace some of the water). Then blow it off with an air compressor around 40psi (this is important so that the water and sediments don't settle under ICs and components), and finally when no more liquids can be blown off, let it air dry for an hour and inspect it to make sure no residue has been left behind. If there is still residue, repeat some of the cleaning as necessary. Otherwise, let the board fully dry for about a day.

_{Post edited by ForceFlow: clarifications}

You should really remove fuses, socketed chips and relays (if applicable). Scrubbing bubbles works better than simple green IMO.

https://pinside.com/pinball/forum/topic/clean-circuit-boards

Per my discussion in PM with the OP, this is likely heat damage. It shows up more frequently on Sys11 and previous power supplies, and sometimes on dot matrix drivers, when cleaned with most chemicals and water. I've tried numerous chemicals, mixes, etc and I have not found a way to clean a board using water that doesn't do this, if the board has significant heat damage.

When you look at where it's located (around the GI triac heatsinks, under the LM323), it's at the hottest parts of the board, and a few spots where someone has soldered on the board.

The only way I've had decent luck 'removing' it is with acetone. Smelly, flammable, and not really a lot of fun. But does a pretty good job. Do this outdoors!

I wash PCBs similar to how is described here. On boards after Sys11, I've had good luck leaving relays installed. I don't know if they started sealing relays better at some point or what. On Sys11 and older boards, I desolder and remove relays before cleaning boards.

I usually remove the relays and throw the boards in the dishwasher.

I have seen guides on the net that show just sealing the relay with a length of scotch tape where the clear hood meets the base, and then dishwashing them.