Hi Cartwheel,
just as an extra couple of questions, you say that once the coins are in the coin holders then they are stored flat in coin trays. How are your coin tray then stored, are they in a cupboard or left out somewhere?
The reason I am asking is it may be another factor that is causing the toning especially as you say it's often on one side.
I would have guessed that Lighthouse would have become aware if there was a problem with their holders or the adhesive they are using. Are they genuine Lighhouse holders?
Just trying to eliminate possibility
Ian