Thompson's sealer is actually like buying bottled water. that stuff has the viscosity of water and does not last long at all. I would say that the properties of that stuff will only be around for about 3 months tops after application.
What you may be encountering is sap or drippings from the wood itself. If its wolmanized decking, the nail holes may be oozing CCA or CCA and sap onto the decking below.
I would suggest to use some heavy industrial cleaner that works on grease. I would first try some bleach and water and then spread some comet on the surface and then scrub brush it. You need to cut the goo.
Try some White Vinegar. This is a mild muratic acid and might cut it and not be as strong as other stuff.