I also re-mounted the running board channel and tread runners last year after the paintwork under the aluminium channel was blistering up around each mounting bolt on both sides of the car.
I thought it may have been galvanic action as the fixing nuts & bolts are stainless, Dave W suggested the probable cause was moisture ingress in the bolt holes under the 2E paint.
On re-fitting I made sure the oversized holes in the running boards had lots of primer added also Duralac was applied and a small round beading, ‘O’ ring of plumbers putty around each bolt was applied sealing the assembly .
I also used a strip of 1.5mm thick mounting rubber between the aluminium channel and the running board, this was a ‘Neo Strip Fixing Kit’ 15mm x 1.5mm 5mtr including Alpha Thixofix adhesive which I used to glue the strip to the aluminium, I purchased the kit from Delta Rubber.

David, 2001 4/4 4seater Avus Blue