I’ve seen discoloration from heat as well. Are the spots near the center of the floor? If so, could be from heat caused by the furnace ducting below the flooring. Obviously, this would be much different than marker bleed through. The discoloration would be more blotchy.
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Brent
2013 Alpine 3500RE
2019 Silverado 2500HD Duramax
U.S. Air Force Retired (25 yrs)
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