The black stain in the water has to be coming from somewhere and caused by something. The question is where and what?

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Leaks sometimes are not easy to find. They can show up in one spot, but the source can come from another area far away.

There are acceptable methods for installing ceramic tile over wood substrates in interior dry applications. It is always considered better to install over a mortar bed or over one of the approved tile backer boards.

The leaking of deck causing damages in the ceiling below is the symptom of the cause of the problem. Treating the symptom will not remediate the cause of the problem.

Grout joints within a tile installation are always going to vary to some degree as the installer makes adjustments for the sizing variation of the tile. Rectified tiles will be more consistent in sizing.

First of all you don’t really need to seal your grout. I assume it is a cementitious grout, which is porous. Put generally speaking you don’t have to seal it. It will get darker over time whether you seal it or not, but it will be easier to clean and will less likely stain if you do seal it.

If the tile assembly is properly installed you can use an ASTM C920 sealant in lieu of cementitious grout with some limitations.

Industry standards do not recommend butting tiles together whether they are a stone tile or a ceramic tile.