After looking at it, it’s not really leaking or dripping, more so just a little moisture around the seal.

Heat and moisture gets trapped under the house and the heat wants to rise but the LVP creates a vaporlock, thus inhibiting the mold growth. 

My GC primed and painted over them a few times thinking they were just old, stubborn stains that needed extra product, but they kept coming back after each rainfall.I hired a water intrusion detection company to help me pinpoint the problem - they said the new roof seemed solid and that based on infrared and temperature readings, the moisture is coming in from the partition walls.

There were temporary support beams in the basement along with enough moisture to actually grow mushrooms in the basement crevices!  

The first part of Mold remediating is stopping the moisture issue  until you figure out that part don't bother with step 2 . 

They also make those moisture meters, that I have had roofers use in my attics to attempt to trace back sources.As noted, in my market, if you have active leaks that you are aware of, they need to be disclosed when selling a property.  

Mold requires moisture and a food source (dust is sufficient).

They pull any moisture they can get out of the air, so if there are any small cracks or openings to outside air they will just continue running, filling up their tank from the moisture in the outside air and not working efficiently at drying out the space you’re trying to dry very well.

@Tony Sherman, yes.Closing delays on buy side with title issuesMaterial delays, which can compound into contractor delays when you try to keep schedules tightContractor delays because prior jobs are not wrapping on timeContractor delays because you need to fire one and hire a new oneScope of work issues, i.e. no signs of moisture intrusion prior to buying, but all of a sudden you have a wet floor after a good hard rain.Closing issues on sale sideHow do you manage?  

We also tiled the entire first level because the property is partially built into a hill and this would help reduce moisture issues.We also added a stacked laundry center by the front entrance.