It can be hard to clean sugar (coolant) off of metal, especially metal that is porous. I've noticed many times the RTV comes off of the old pieces easier than it should, which leads me to believe it never bonded well in the first place. Really hot water and soap is best for cleaning off coolant, Window cleaner spray works in a pinch, brake cleaner and solvents not so well.
I lay a sheet of 400 sand paper on something flat and take a couple of swipes with the thermo housing on the sand paper. Low spots, high spots and missed chunks of old gasket show up quick.
Best guess is sometime in the past the thermo housing was over tightened and is now bowed or there is a hairline crack in either the housing or the block. And/or the housing had been way over tightened in the past has has raised/ridged the very edge of the bolt hole in the block. A quick cleaning with a counter sink will remove the ridge. I can usually feel that ridge ridge with my finger tip, where my eyes may not be good enough to see it.
If you can get the crack cleaned well enough, epoxy can get the crack sealed. But like I mentioned coolant specially coolant soaked into a porous metal can be hard to clean. Repeated cleaning with soap and near boiling water usually works best. I've used JB Weld, Permatex multi metal epoxy, or Loc Tite epoxy. The trick is to find an epoxy that bonds well but isn't overly brittle, so it survives heat and cool cycles.
Don't discount a casting flaw and/or a tiny pinhole as being the culprit. The pinhole can be a significant distance from where the stain appears as they tend to spray. Pinhole leaks are fairly common in cast aluminum parts.
The thermo housing bolt holes go all the way through the block into the water jacket (most times). Clean out the bolt holes and use a sealer on the bolt threads.